diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..a6a0ad1 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,13 @@ +data/ecoli_trna_scan.tar filter=lfs diff=lfs merge=lfs -text +data/k2_subset_with_rfam_consensus.tar filter=lfs diff=lfs merge=lfs -text +data/k2.tgz filter=lfs diff=lfs merge=lfs -text +data/README filter=lfs diff=lfs merge=lfs -text +data/Rfam_local.tar filter=lfs diff=lfs merge=lfs -text +data/rfam_pool.fa filter=lfs diff=lfs merge=lfs -text +data/semi_global_pvalue.tar filter=lfs diff=lfs merge=lfs -text +examples/ecoli_MG1655.fa filter=lfs diff=lfs merge=lfs -text +examples/RF00167_1_nogap.ref filter=lfs diff=lfs merge=lfs -text +examples/RF00167_1.raw filter=lfs diff=lfs merge=lfs -text +examples/RF00167_1.ref filter=lfs diff=lfs merge=lfs -text +examples/trna.fa filter=lfs diff=lfs merge=lfs -text +examples/tRNAscan.fa filter=lfs diff=lfs merge=lfs -text diff --git a/src/Makefile b/src/Makefile new file mode 100644 index 0000000..e85b2ae --- /dev/null +++ b/src/Makefile @@ -0,0 +1,50 @@ +CXX = g++ +#CXXFLAGS = -g -DDEBUG +LDFLAGS = -L. -lm -lRNA +all: RNAmountAlignScan RNAmountAlign + +RNAmountAlignScan: RNAmountAlignScan.o pair_align.o arguments.o aux.o mountain_height.o evd.o stats.o karlin_altschul.o + ${CXX} ${CXXFLAGS} -o RNAmountAlignScan RNAmountAlignScan.o pair_align.o arguments.o aux.o mountain_height.o evd.o stats.o karlin_altschul.o ${LDFLAGS} + +RNAmountAlign: RNAmountAlign.o pair_align.o arguments.o aux.o mountain_height.o stats.o karlin_altschul.o evd.o multi_align.o profile.o profile_aligner.o + ${CXX} ${CXXFLAGS} -o RNAmountAlign RNAmountAlign.o pair_align.o arguments.o aux.o mountain_height.o stats.o karlin_altschul.o evd.o multi_align.o profile.o profile_aligner.o ${LDFLAGS} + +RNAmountAlignScan.o:RNAmountAlignScan.cpp RNAmountAlignScan.h arguments.h pair_align.h mountain_height.h aux.h evd.h stats.h karlin_altschul.h + ${CXX} ${CXXFLAGS} -c RNAmountAlignScan.cpp + +RNAmountAlign.o:RNAmountAlign.cpp arguments.h pair_align.h mountain_height.h aux.h + ${CXX} ${CXXFLAGS} -c RNAmountAlign.cpp + +pair_align.o:pair_align.cpp aux.h aux.cpp + ${CXX} ${CXXFLAGS} -c pair_align.cpp + +arguments.o:arguments.cpp aux.h + ${CXX} ${CXXFLAGS} -c arguments.cpp + +aux.o:aux.cpp pair_align.cpp + ${CXX} ${CXXFLAGS} -c aux.cpp + +mountain_height.o:mountain_height.cpp + ${CXX} ${CXXFLAGS} -c mountain_height.cpp + +stats.o:stats.cpp stats.h + ${CXX} ${CXXFLAGS} -c stats.cpp + +evd.o:evd.cpp evd.h + ${CXX} ${CXXFLAGS} -c evd.cpp + +karlin_altschul.o: karlin_altschul.cpp karlin_altschul.h + ${CXX} ${CXXFLAGS} -c karlin_altschul.cpp + +multi_align.o:multi_align.cpp multi_align.h aux.h profile_aligner.h profile_aligner.h pair_align.h + ${CXX} ${CXXFLAGS} -c multi_align.cpp + +profile_aligner.o:profile_aligner.cpp profile_aligner.h aux.h aux.cpp profile_aligner.h profile_aligner.cpp + ${CXX} ${CXXFLAGS} -c profile_aligner.cpp + + +profile.o:profile.cpp profile.h aux.h aux.cpp + ${CXX} ${CXXFLAGS} -c profile.cpp + +clean: + rm -fr *.o RNAmountAlignScan RNAmountAlign diff --git a/src/README.txt b/src/README.txt new file mode 100755 index 0000000..e338122 --- /dev/null +++ b/src/README.txt @@ -0,0 +1,160 @@ +Amir Bayegan, Peter Clote --Boston College + +/****************************************************************************** + * Copyright (C) 2018 Amir Bayegan, Peter Clote * + * * + * This program is free software: you can redistribute it and/or modify * + * it under the terms of the GNU General Public License as published by * + * the Free Software Foundation, either version 3 of the License, or * + * (at your option) any later version. * + * * + * This program is distributed in the hope that it will be useful, * + * but WITHOUT ANY WARRANTY; without even the implied warranty of * + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * + * GNU General Public License for more details. * + * * + * You should have received a copy of the GNU General Public License * + * along with this program. If not, see . * + ******************************************************************************/ + +RNAmountAlign performs a local/semi-global/global sequence structure alignment. + +RNAmountAlignScan executable is used for searching a query in a given target sequence. + +Statistics are reported based on the alignment type either from Karlin-Altschul +or parameter fitting(see the paper). + + +Running the program: + +Executables: + RNAmountAlign + RNAmountAlignScan + +WARNING: The current libRNA.a is compiled for Linux systems. + If there is a problem with linking the library, please download + and compile Vienna RNA Package on your system and replace + the current libRNA.a with the one obtained from Vienna. + +Usage: ./RNAmountAlign [options] +REQUIRED: + RNAmountAlign: + -f the input fasta file containing two sequences + OR + -s provide sequence1 and sequence2 + + +OPTIONS: + +ALIGNMENT: + -gi Gap initiation penalty for sequence alignment(Default:-3). + A negative value should be provided + + -ge Gap extension penalty for sequence alignment(Default:-1). + A negative value should be provided + + -gamma Weight of the structural homology. Must be in [0,1](Default:0.5) + similarity = gamma*str_sim + (1-gamma)*seq_sim + + -m Similarity matrix file in RIBOSUM format.(Default:RIBOSUM85-60.mat) + All RIBOSUM files are included in ./matrices directory + + -semi Perform semi-global alignment. + Both gap ends of the firts sequence will be free of penalty. + + -local Perform local alignment + + -global Perform global alignment.(Default alignment type) + + -alifold Output the consensus structure of the alignment from RNAalifold + + +STATISTICS: + KA=Karlin-Altschul; EVD=extreme value dirstribution, ND=normal distribution + + -stat Report statistics based on the alignment type(Default: off). + For local alignments: E-value from Karlin-Altschul(default) or EVD fitting + For global alignments: p-value from ND fitting + For semi-global alignments: p-value from ND fitting + + -evd EVD fitting will be used for local alignments instead of KA + + -num Number of random sequences generated for fitting.(Default:500) + + -gc Size of GC bins (an integer between [0-100]). (Default: 5) + This is used only with with parameter fitting and not KA. + + +OUTPUT: + -o Write the output to a file. + If not used the output will be printed to stdout. + + -format Format of the alignment output. (Default: clustal) + + -v Verbose output. Prints MFE structures, the ensmeble expected and incremental heights. + + -h Print help + +/******************************************************************************** + +Usage: ./RNAmountAlignScan [options] +REQUIRED: + RNAmountAlignScan: + -qf fasta file containing query sequence + AND + -tf fasta file containing target sequence + + +OPTIONS: + +SLIDING + -window Size of the sliding window(Default:300). + + -step Step size for incrementing the window start(Default:200). + + +ALIGNMENT: + -gi Gap initiation penalty for sequence alignment(Default:-3). + A negative value should be provided + + -ge Gap extension penalty for sequence alignment(Default:-1). + A negative value should be provided + + -gamma Weight of the structural homology. Must be in [0,1](Default:0.5) + similarity = gamma*str_sim + (1-gamma)*seq_sim + + -m Similarity matrix file in RIBOSUM format.(Default:RIBOSUM85-60.mat) + All RIBOSUM files are included in ./matrices directory + + -semi Perform semi-global alignment. + Both gap ends of the firts sequence will be free of penalty. + + -local Perform local alignment + + -global Perform global alignment.(Default alignment type) + + +STATISTICS: + KA=Karlin-Altschul; EVD=extreme value dirstribution, ND=normal distribution + + -stat Report statistics based on the alignment type(Default: off). + For local alignments: E-value from Karlin-Altschul or EVD fitting + For global alignments: p-value from ND fitting + For semi-global alignments: p-value from ND fitting + + -evd EVD fitting will be used for local alignments instead of KA + + -num Number of random sequences generated for fitting.(Default:500) + + -gc Size of GC bins (an integer between [0-100]). (Default: 5) + This is used only with with parameter fitting and not KA. + + +OUTPUT: + -o Write the output to a file. + If not used the output will be printed to stdout. + + -format Format of the alignment output. (Default: clustal) + + -v Verbose output. Prints MFE structures, the ensmeble expected and incremental heights. + -h Print help diff --git a/src/RNAmountAlign.cpp b/src/RNAmountAlign.cpp new file mode 100644 index 0000000..bc9f97d --- /dev/null +++ b/src/RNAmountAlign.cpp @@ -0,0 +1,188 @@ +#include +#include +#include +#include +#include +#include "arguments.h" +#include "pair_align.h" +#include "multi_align.h" +#include "mountain_height.h" +#include "aux.h" +#include "stats.h" + +char outtxt[1000000]; + +int main(int argc , char * argv[]){ + int m,i; + //parse the input parameters + Arguments args; + args.parseArgs(argc,argv); + m =args.seqs.size(); + vector aln; + string a = args.sprintArgs().c_str(); + strcat(outtxt,a.c_str()); + if(args.seqs.size()==2){//pairwise alignment + double evalue,pval; + int n1 = args.seqs[0].length(); + int n2 = args.seqs[1].length(); + + vector > gc_mu_lam_vec; //stores mu and lambda for each gc bin + //compute expected heights + double ** bppr1 = allocate2DdoubleArray(n1,n1+1); + double ** bppr2 = allocate2DdoubleArray(n2,n2+1); + double MFE1,ensEng1,MFE2,ensEng2; + char * s1 = new char[n1+1]; + char * s2 = new char[n2+1]; + char * mfeStr1 = new char[n1+1]; + char * mfeStr2 = new char[n2+1]; + strcpy(s1,args.seqs[0].c_str()); + strcpy(s2,args.seqs[1].c_str()); + vector h1,h2,raw_h1,raw_h2; + BasePairProbabilities(s1,n1,&MFE1,mfeStr1,&ensEng1,argv[0],bppr1); + BasePairProbabilities(s2,n2,&MFE2,mfeStr2,&ensEng2,argv[0],bppr2); + if(args.modified_height){ + raw_h1 = expectedModifiedHeight(bppr1,n1); + raw_h2 = expectedModifiedHeight(bppr2,n2); + } + else{ + raw_h1 = expectedHeight(bppr1,n1); + raw_h2 = expectedHeight(bppr2,n2); + } + + h1 = heightDiff(raw_h1); + h2 = heightDiff(raw_h2); + + //Align the sequences + Alignment aligner(args.seqs[0],args.seqs[1],h1,h2,bppr1,bppr2,args); + aligner.align(); + + //Statistics + if(args.stats and args.aln_type=='l'){ + if(args.evd){ + vector gc_vec; + gc_vec.push_back(getGCcontent(args.seqs[0])); + computeStats_bin_gc(args,gc_vec,gc_mu_lam_vec,'E'); + evalue = computeEvalue_EVD(aligner.getScore(),gc_mu_lam_vec[0][3],gc_mu_lam_vec[0][2]); + pval = Eval2Pval(evalue); + } + else{ + vector nucpr1, nucpr2; + double k,lambda; + getNucleotideProbabilities(s1,nucpr1); + getNucleotideProbabilities(s2,nucpr2); + karlinStats(nucpr1,bppr1,n1,nucpr2,bppr2,n2,args.subMat,args.str_weight,k,lambda); + evalue = computeEvalue(aligner.getScore(),lambda,k,n1*n2); + evalue = KAevalueRegressionTransform(evalue); + pval = Eval2Pval(evalue); + } + } + else if(args.stats){ + vector gc_vec; + gc_vec.push_back(getGCcontent(args.seqs[0])); + computeStats_bin_gc(args,gc_vec,gc_mu_lam_vec,'N'); + pval = computePvalueNormal(aligner.getScore(),gc_mu_lam_vec[0][3],gc_mu_lam_vec[0][2]); + evalue = Pval2Eval(pval); + } + + // Output + if(verbose){ + sprintf(outtxt+strlen(outtxt),"#%s:\n%s\n%s (%f)\n",args.ids[0].c_str(),args.seqs[0].c_str(),mfeStr1,MFE1); + sprintf(outtxt+strlen(outtxt),"#%s:\n%s\n%s (%f)\n",args.ids[1].c_str(),args.seqs[1].c_str(),mfeStr2,MFE2); + sprintf(outtxt+strlen(outtxt),"\n#Ensemble expected heights:\n#%s:",args.ids[0].c_str()); + strcat(outtxt,sprintHeights(raw_h1).c_str()); + sprintf(outtxt+strlen(outtxt),"#%s:",args.ids[1].c_str()); + strcat(outtxt,sprintHeights(raw_h2).c_str()); + sprintf(outtxt+strlen(outtxt),"\n#Ensemble incremental heights:\n#%s:",args.ids[0].c_str()); + strcat(outtxt,sprintHeights(h1).c_str()); + sprintf(outtxt+strlen(outtxt),"#%s:",args.ids[1].c_str()); + strcat(outtxt,sprintHeights(h2).c_str()); + } + if(args.stats and args.aln_type=='l'){ + if(args.evd){ + sprintf(outtxt+strlen(outtxt),"\n#Statistics:\nNumber of random alignments: %d\n",args.rnd_num); + sprintf(outtxt+strlen(outtxt),"Random alignment scores: mean= %f;std= %f\n",gc_mu_lam_vec[0][2],gc_mu_lam_vec[0][3]); + sprintf(outtxt+strlen(outtxt),"Extreme value distribution E-value: %f \n",evalue); + sprintf(outtxt+strlen(outtxt),"Extreme value distribution P-value: %f \n",pval); + } + else{ + sprintf(outtxt+strlen(outtxt),"\n#Statistics:\nExtreme value distribution E-value: %f \n",evalue); + sprintf(outtxt+strlen(outtxt),"Extreme value distribution P-value: %f \n",pval); + } + } + else if(args.stats){ + sprintf(outtxt+strlen(outtxt),"\n#Statistics:\nNumber of random alignments: %d\n",args.rnd_num); + sprintf(outtxt+strlen(outtxt),"Random alignment scores: mean= %f;std= %f\n",gc_mu_lam_vec[0][2],gc_mu_lam_vec[0][3]); + sprintf(outtxt+strlen(outtxt),"Normal distribution E-value: %f \n",evalue); + sprintf(outtxt+strlen(outtxt),"Normal distribution P-value: %f \n",pval); + } + a=aligner.sprintAlignment(); + strcat(outtxt+strlen(outtxt),a.c_str()); + aln.push_back(aligner.getSeq1()); + aln.push_back(aligner.getSeq2()); + + + free2DdoubleArray(bppr1,n1); + free2DdoubleArray(bppr2,n2); + delete [] s1; + delete [] s2; + delete [] mfeStr1; + delete [] mfeStr2; + } + else{ //multiple alignment + aln = multi_align(args); + } + + if(args.alifold){ + double cons_mfe; + int n = aln[0].length(); + char * cons_str = new char[n+1]; + vector cstring_aln; + cstring_aln.reserve(aln.size()+1); + for(int i = 0; i < aln.size(); ++i) + cstring_aln.push_back(aln[i].c_str()); + cstring_aln[aln.size()]="\0"; + runAlifold(&cstring_aln[0], cons_str, cons_mfe); + string cons(cons_str); + const char * id="CONS_STR"; + if (args.outformat=="clustal") + { + int c = n / LINLEN; + int d = n % LINLEN; + int start=0; + for(int i=0;i0){ + sprintf(outtxt+strlen(outtxt),"%-15s %-6s (%-5.2f)\n",id,cons.substr(start,d).c_str(),cons_mfe); + } + } + else if(args.outformat=="fasta"){ + int c = n / LINLEN; + int d = n % LINLEN; + int start=0; + sprintf(outtxt+strlen(outtxt),">CONS_STR\n"); + for(int i=0;i0){ + sprintf(outtxt+strlen(outtxt),"%s\n",cons.substr(start,LINLEN).c_str()); + } + } + delete cons_str; + } + if(args.output_name==""){ + cout << outtxt; + } + else{ + ofstream outfile; + outfile.open(args.output_name.c_str()); + outfile << outtxt; + outfile.close(); + } + return 0; +} + + + diff --git a/src/RNAmountAlignScan.cpp b/src/RNAmountAlignScan.cpp new file mode 100644 index 0000000..4357b50 --- /dev/null +++ b/src/RNAmountAlignScan.cpp @@ -0,0 +1,174 @@ +#include "RNAmountAlignScan.h" + + + +int main(int argc , char * argv[]){ + double ** bppr; + char * mfeStr; + double MFE,ensEng; + char * s; + int n,m,i,w; + vector window_vec; + Window window; + string curr_seq; + double lambda,mu,K,sp; + vector nucpr1,nucpr2; + //parse the input parameters + Arguments args; + args.parseArgs(argc,argv); + m =args.seqs.size(); + + args.printArgs(); + + + if(args.seqs.size()==2){//only 2 sequences in the input + int n1 = args.seqs[0].length(); + int n2 = args.seqs[1].length(); + if (args.window_size>n2){ + args.window_size = n2; + } + + //variables for computing expected heights + double ** bppr1 = allocate2DdoubleArray(n1,n1+1); + double MFE2,ensEng2,MFE1,ensEng1; + char * s1 = new char[n1+1]; + char * mfeStr1 = new char[n1+1]; + strcpy(s1,args.seqs[0].c_str()); + vector h1,h2; + + + if (n2n2-1){ + w = n2-i; + if(w gc_vec; //stores gc content of each window in reference + vector > gc_mu_lam_vec; //stores mu and lambda for each gc bin + for(i=0;i::iterator it=window_vec.begin(); it!= window_vec.end(); ++it){ + printf("%-12.2f\t%-12d\t%-12d\t%-12d\t%-12d\t%-12e\n",it->score,it->start,it->end,it->aln_pos[2]+it->start-1,it->aln_pos[3]+it->start-1,it->evalue); + } + } + else{//local + if(args.evd){ + vector gc_vec; //stores gc content of each window in reference + vector > gc_mu_lam_vec; //stores mu and lambda for each gc bin + for(i=0;i::iterator it=window_vec.begin(); it!= window_vec.end(); ++it){ + printf("%-12.2f\t%-12d\t%-12d\t%-12d\t%-12d\t%-12e\n",it->score,it->start,it->end,it->aln_pos[2]+it->start-1,it->aln_pos[3]+it->start-1,it->evalue); + } + } + else{//karlin-altschul + for(i=0;i::iterator it=window_vec.begin(); it!= window_vec.end(); ++it){ + printf("%-12.2f\t%-12d\t%-12d\t%-12d\t%-12d\t%-12e\n",it->score,it->start,it->end,it->aln_pos[2]+it->start-1,it->aln_pos[3]+it->start-1,it->karlin_evalue); + } + } + } + } + else{//output only alignment scores + printf("#Window Size:%d; Step Size:%d\n\n#Hits:\n",args.window_size,args.step_size); + printf("%-12s\t%-12s\t%-12s\t%-12s\t%-12s\n","Score","Window_Begin","Window_End","Aln_Begin","Aln_end"); + for (vector::iterator it=window_vec.begin(); it!= window_vec.end(); ++it){ + printf("%-12.2f\t%-12d\t%-12d\t%-12d\t%-12d\n",it->score,it->start,it->end,it->aln_pos[2]+it->start-1,it->aln_pos[3]+it->start-1); + } + } + + delete [] s1; + delete [] mfeStr1; + free2DdoubleArray(bppr1,n1); + } + return 0; +} + + + diff --git a/src/RNAmountAlignScan.h b/src/RNAmountAlignScan.h new file mode 100644 index 0000000..779eb17 --- /dev/null +++ b/src/RNAmountAlignScan.h @@ -0,0 +1,41 @@ +#ifndef RNAMOUNTALIGNSCAN_H_ +#define RNAMOUNTALIGNSCAN_H_ +#include +#include +#include +#include +#include "arguments.h" +#include "pair_align.h" +#include "mountain_height.h" +#include "aux.h" +#include "evd.h" +#include "stats.h" + + +struct Window{ + vector aln_pos; + int index; //starts from 0 + int start; //1-indexed + int end; //1-indexed + float gc; + double lambda; + double mu; + double karlin_k; + double karlin_lambda; + double karlin_evalue; + double evalue; + double score; + string seq; + void print(); +}; + +void Window::print(){ + printf("window:%d,(%d,%d),GC:%.2f,lambda:%.2f,mu:%.2f,eval:%e\n",index,start,end,gc,lambda,mu,evalue); +} +// overload operator < to compare objects by Evalue +bool operator < ( const Window & l, const Window & r){ + return l.evalue < r.evalue; + } + + +#endif /* RNAMOUNTALIGNSCAN_H_ */ diff --git a/src/RNAstruct.h b/src/RNAstruct.h new file mode 100644 index 0000000..aa65e26 --- /dev/null +++ b/src/RNAstruct.h @@ -0,0 +1,152 @@ +#ifndef __VIENNA_RNA_PACKAGE_RNASTRUCT_H__ +#define __VIENNA_RNA_PACKAGE_RNASTRUCT_H__ + +/** + * \file RNAstruct.h + * \brief Parsing and Coarse Graining of Structures + * + * Example: + * \verbatim + * .((..(((...)))..((..)))). is the bracket or full tree + * becomes expanded: - expand_Full() - + * ((U)(((U)(U)((((U)(U)(U)P)P)P)(U)(U)(((U)(U)P)P)P)P)(U)R) + * HIT: - b2HIT() - + * ((U1)((U2)((U3)P3)(U2)((U2)P2)P2)(U1)R) + * Coarse: - b2C() - + * ((H)((H)M)R) + * becomes expanded: - expand_Shapiro() - + * (((((H)S)((H)S)M)S)R) + * weighted Shapiro: - b2Shapiro() - + * ((((((H3)S3)((H2)S2)M4)S2)E2)R) + * \endverbatim + */ + +#define STRUC 2000 + +/** + * \brief Converts the full structure from bracket notation to the HIT + * notation including root. + * + * \param structure + * \return + */ +char *b2HIT(const char *structure); /* Full -> HIT [incl. root] */ + +/** + * \brief Converts the full structure from bracket notation to the a + * coarse grained notation using the 'H' 'B' 'I' 'M' and 'R' identifiers. + * + * \param structure + * \return + */ +char *b2C(const char *structure); /* Full -> Coarse [incl. root] */ + +/** + * \brief Converts the full structure from bracket notation to the + * weighted coarse grained notation using the 'H' 'B' 'I' 'M' 'S' 'E' and + * 'R' identifiers. + * + * \param structure + * \return + */ +char *b2Shapiro(const char *structure); /* Full -> weighted Shapiro [i.r.] */ + +/** + * \brief Adds a root to an un-rooted tree in any except bracket notation. + * + * \param structure + * \return + */ +char *add_root(const char *structure); /* {Tree} -> ({Tree}R) */ + +/** + * \brief Inserts missing 'S' identifiers in unweighted coarse grained structures + * as obtained from b2C(). + * + * \param coarse + * \return + */ +char *expand_Shapiro(const char *coarse); + +/* add S for stacks to coarse struct */ +/** + * \brief Convert the full structure from bracket notation to the + * expanded notation including root. + * + * \param structure + * \return + */ +char *expand_Full(const char *structure); /* Full -> FFull */ + +/** + * \brief Restores the bracket notation from an expanded full or HIT tree, that is + * any tree using only identifiers 'U' 'P' and 'R'. + * + * \param ffull + * \return + */ +char *unexpand_Full(const char *ffull); /* FFull -> Full */ + +/** + * \brief Strip weights from any weighted tree. + * + * \param wcoarse + * \return + */ +char *unweight(const char *wcoarse); /* remove weights from coarse struct */ + +/** + * \brief Converts two aligned structures in expanded notation. + * + * Takes two aligned structures as produced by + * tree_edit_distance() function back to bracket notation with '_' + * as the gap character. The result overwrites the input. + * + * \param align + */ +void unexpand_aligned_F(char *align[2]); + +/** + * \brief Collects a statistic of structure elements of the full structure in + * bracket notation. + * + * The function writes to the following global variables: + * #loop_size, #loop_degree, #helix_size, #loops, #pairs, #unpaired + * + * \param structure + * \return + */ +void parse_structure(const char *structure); /* make structure statistics */ + +/** + * \brief contains a list of all loop sizes. loop_size[0] contains the + * number of external bases. + */ +extern int loop_size[STRUC]; /* loop sizes of a structure */ + +/** + * \brief contains a list of all stack sizes. + */ +extern int helix_size[STRUC]; /* helix sizes of a structure */ + +/** + * \brief contains the corresponding list of loop degrees. + */ +extern int loop_degree[STRUC]; /* loop degrees of a structure */ + +/** + * \brief contains the number of loops ( and therefore of stacks ). + */ +extern int loops; /* n of loops and stacks */ + +/** + * \brief contains the number of unpaired bases. + */ +extern int unpaired; + +/** + * \brief contains the number of base pairs in the last parsed structure. + */ +extern int pairs; /* n of unpaired digits and pairs */ + +#endif diff --git a/src/alifold.h b/src/alifold.h new file mode 100644 index 0000000..ee03092 --- /dev/null +++ b/src/alifold.h @@ -0,0 +1,378 @@ +#ifndef __VIENNA_RNA_PACKAGE_ALIFOLD_H__ +#define __VIENNA_RNA_PACKAGE_ALIFOLD_H__ + +#include "data_structures.h" + +/** + * \addtogroup consensus_fold + * \brief compute various properties (consensus MFE structures, partition function, + * Boltzmann distributed stochastic samples, ...) for RNA sequence alignments + * + * Consensus structures can be predicted by a modified version of the + * fold() algorithm that takes a set of aligned sequences instead + * of a single sequence. The energy function consists of the mean energy + * averaged over the sequences, plus a covariance term that favors pairs + * with consistent and compensatory mutations and penalizes pairs that + * cannot be formed by all structures. For details see \cite hofacker:2002 and + * \cite bernhart:2008. + * @{ + * \file alifold.h + * \brief compute various properties (consensus MFE structures, partition function, Boltzmann + * distributed stochastic samples, ...) for RNA sequence alignments + * + * @} + */ + + +/** + * \addtogroup consensus_mfe_fold + * \ingroup consensus_fold + * @{ + * + * @} + */ + +/** + * \brief This variable controls the weight of the covariance term in the + * energy function of alignment folding algorithms + * + * \ingroup consensus_fold + * + * Default is 1. + */ +extern double cv_fact; +/** + * \brief This variable controls the magnitude of the penalty for non-compatible sequences in + * the covariance term of alignment folding algorithms. + * + * \ingroup consensus_fold + * + * Default is 1. + */ +extern double nc_fact; + +/* +############################################## +# MFE VARIANTS OF THE ALIFOLD IMPLEMENTATION # +############################################## +*/ + +/** + * \brief Update the energy parameters for alifold function + * + * Call this to recalculate the pair matrix and energy parameters after a + * change in folding parameters like #temperature + */ +void update_alifold_params(void); + + +/** + * \brief Compute MFE and according consensus structure of an alignment of sequences + * + * This function predicts the consensus structure for the aligned 'sequences' + * and returns the minimum free energy; the mfe structure in bracket + * notation is returned in 'structure'. + * + * Sufficient space must be allocated for 'structure' before calling + * alifold(). + * + * \ingroup consensus_mfe_fold + * + * \param strings A pointer to a NULL terminated array of character arrays + * \param structure A pointer to a character array that may contain a constraining consensus structure + * (will be overwritten by a consensus structure that exhibits the MFE) + * \return The free energy score in kcal/mol + */ +float alifold( const char **strings, + char *structure); + + +/** + * \brief Compute MFE and according structure of an alignment of sequences assuming the sequences are circular instead of linear + * + * \ingroup consensus_mfe_fold + * + * \param strings A pointer to a NULL terminated array of character arrays + * \param structure A pointer to a character array that may contain a constraining consensus structure + * (will be overwritten by a consensus structure that exhibits the MFE) + * \return The free energy score in kcal/mol + */ +float circalifold( const char **strings, + char *structure); + +/** + * \brief Free the memory occupied by MFE alifold functions + * + * \ingroup consensus_mfe_fold + * + */ +void free_alifold_arrays(void); + +/** + * \brief Get the mean pairwise identity in steps from ?to?(ident) + * + * \ingroup consensus_fold + * + * \param Alseq + * \param n_seq The number of sequences in the alignment + * \param length The length of the alignment + * \param mini + * \return The mean pairwise identity + */ +int get_mpi(char *Alseq[], + int n_seq, + int length, + int *mini); + +/** + * \brief Read a ribosum or other user-defined scoring matrix + * + * \ingroup consensus_fold + * + */ +float **readribosum(char *name); + +/** + * \brief Calculate the free energy of a consensus structure given a set of aligned sequences + * + * \ingroup consensus_fold + * + * \param sequences The NULL terminated array of sequences + * \param structure The consensus structure + * \param n_seq The number of sequences in the alignment + * \param energy A pointer to an array of at least two floats that will hold the free energies + * (energy[0] will contain the free energy, energy[1] will be filled with the covariance energy term) + * \returns free energy in kcal/mol + * + */ +float energy_of_alistruct(const char **sequences, + const char *structure, + int n_seq, + float *energy); + +float energy_of_ali_gquad_structure(const char **sequences, + const char *structure, + int n_seq, + float *energy); + +/* +############################################################# +# some helper functions that might be useful in the library # +############################################################# +*/ + +/** + * \brief Get arrays with encoded sequence of the alignment + * + * this function assumes that in S, S5, s3, ss and as enough + * space is already allocated (size must be at least sequence length+2) + * + * \ingroup consensus_fold + * + * \param sequence The gapped sequence from the alignment + * \param S pointer to an array that holds encoded sequence + * \param s5 pointer to an array that holds the next base 5' of alignment position i + * \param s3 pointer to an array that holds the next base 3' of alignment position i + * \param ss + * \param as + * \param circ assume the molecules to be circular instead of linear (circ=0) + */ +void encode_ali_sequence( const char *sequence, + short *S, + short *s5, + short *s3, + char *ss, + unsigned short *as, + int circ); + +/** + * \brief Allocate memory for sequence array used to deal with aligned sequences + * + * Note that these arrays will also be initialized according to the sequence alignment given + * + * \ingroup consensus_fold + * + * \see free_sequence_arrays() + * + * \param sequences The aligned sequences + * \param S A pointer to the array of encoded sequences + * \param S5 A pointer to the array that contains the next 5' nucleotide of a sequence position + * \param S3 A pointer to the array that contains the next 3' nucleotide of a sequence position + * \param a2s A pointer to the array that contains the alignment to sequence position mapping + * \param Ss A pointer to the array that contains the ungapped sequence + * \param circ assume the molecules to be circular instead of linear (circ=0) + */ +void alloc_sequence_arrays(const char **sequences, + short ***S, + short ***S5, + short ***S3, + unsigned short ***a2s, + char ***Ss, + int circ); + +/** + * \brief Free the memory of the sequence arrays used to deal with aligned sequences + * + * This function frees the memory previously allocated with alloc_sequence_arrays() + * + * \ingroup consensus_fold + * + * \see alloc_sequence_arrays() + * + * \param n_seq The number of aligned sequences + * \param S A pointer to the array of encoded sequences + * \param S5 A pointer to the array that contains the next 5' nucleotide of a sequence position + * \param S3 A pointer to the array that contains the next 3' nucleotide of a sequence position + * \param a2s A pointer to the array that contains the alignment to sequence position mapping + * \param Ss A pointer to the array that contains the ungapped sequence + */ +void free_sequence_arrays( unsigned int n_seq, + short ***S, + short ***S5, + short ***S3, + unsigned short ***a2s, + char ***Ss); + +/* +############################################################# +# PARTITION FUNCTION VARIANTS OF THE ALIFOLD IMPLEMENTATION # +############################################################# +*/ + + +/** + * \addtogroup consensus_pf_fold + * \ingroup consensus_fold + * @{ + * + * @} + */ + +/** + * \brief + * + * \ingroup consensus_pf_fold + * + * \param sequences + * \param structure + * \param pl + * \param parameters + * \param calculate_bppm + * \param is_constrained + * \param is_circular + * \return + */ +float alipf_fold_par( const char **sequences, + char *structure, + plist **pl, + pf_paramT *parameters, + int calculate_bppm, + int is_constrained, + int is_circular); + +/** + * \brief + * + * The partition function version of alifold() works in analogy to + * pf_fold(). Pair probabilities and information about sequence + * covariations are returned via the 'pi' variable as a list of + * #pair_info structs. The list is terminated by the first entry with + * pi.i = 0. + * + * \ingroup consensus_pf_fold + * + * \param sequences + * \param structure + * \param pl + * \return + */ +float alipf_fold( const char **sequences, + char *structure, + plist **pl); + +/** + * \brief + * + * \ingroup consensus_pf_fold + * + * \param sequences + * \param structure + * \param pl + * \return + */ +float alipf_circ_fold(const char **sequences, + char *structure, + plist **pl); + + +/** + * \brief Get a pointer to the base pair probability array + * + * Accessing the base pair probabilities for a pair (i,j) is achieved by + * \verbatim FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; \endverbatim + * + * \ingroup consensus_pf_fold + * + * \see get_iindx() + * \return A pointer to the base pair probability array + */ +FLT_OR_DBL *export_ali_bppm(void); + +/** + * \brief + * + * \ingroup consensus_pf_fold + * + */ +void free_alipf_arrays(void); + +/** + * \addtogroup consensus_stochbt + * @{ + * + * @} + */ + +/** + * \brief Sample a consensus secondary structure from the Boltzmann ensemble according its probability\n + * + * \ingroup consensus_stochbt + * + * \param prob to be described (berni) + * \return A sampled consensus secondary structure in dot-bracket notation + */ +char *alipbacktrack(double *prob); + + +/** + * \brief Get pointers to (almost) all relavant arrays used in alifold's partition function computation + * + * \ingroup consensus_fold + * + * \note To obtain meaningful pointers, call alipf_fold first! + * + * \see pf_alifold(), alipf_circ_fold() + * + * \param S_p A pointer to the 'S' array (integer representation of nucleotides) + * \param S5_p A pointer to the 'S5' array + * \param S3_p A pointer to the 'S3' array + * \param a2s_p A pointer to the pair type matrix + * \param Ss_p A pointer to the 'Ss' array + * \param qb_p A pointer to the QB matrix + * \param qm_p A pointer to the QM matrix + * \param q1k_p A pointer to the 5' slice of the Q matrix (\f$q1k(k) = Q(1, k)\f$) + * \param qln_p A pointer to the 3' slice of the Q matrix (\f$qln(l) = Q(l, n)\f$) + * \return Non Zero if everything went fine, 0 otherwise + */ +int get_alipf_arrays(short ***S_p, + short ***S5_p, + short ***S3_p, + unsigned short ***a2s_p, + char ***Ss_p, + FLT_OR_DBL **qb_p, + FLT_OR_DBL **qm_p, + FLT_OR_DBL **q1k_p, + FLT_OR_DBL **qln_p, + short **pscore); + +#endif diff --git a/src/arguments.cpp b/src/arguments.cpp new file mode 100644 index 0000000..288d9b6 --- /dev/null +++ b/src/arguments.cpp @@ -0,0 +1,511 @@ +#include "arguments.h" + + +Arguments::Arguments(){ + gap_init = -3; + gap_ext = -1; + gap_init_str = -1000; + gap_ext_str = -1000; + str_weight = 0.5; + percentile = 0; + print_prob = false; + normal = false; + eps_name=""; + fasta_name=""; + query_name=""; + target_name=""; + output_name=""; + outformat ="clustal"; + verbose=false; + window_size = 300; + step_size = 200; + rnd_num = 500; + gc_seg = 0.05; + fixed_gamma=true; + modified_height = false; + stats=false; + evd=false; + matrix="matrices/RIBOSUM85-60.mat"; + alifold=false; + qsearch=false; +} +void Arguments::parseArgs(const int argc, char * argv[]){ + if(!(strstr(argv[0],"RNAmountAlignScan"))){ + aln_type='g'; + qsearch=false; + } + else{ + aln_type='q'; + qsearch=true; + } + argv0=argv[0]; + char * execPath = getExecPath(argv0); + strcat(execPath,"/"); + strcat(execPath,matrix); + matrix=execPath; + + if(argc<3){ + printf("error in the input argument!\n"); + printUsage(argv[0]); + } + for(int i=1;i2) + reportErr("Each file must contain a single sequence\n"); + } + loadRibosumMatrix(matrix); + if(gap_init_str==-1000){ //the same structure gap penalties as sequence + gap_init_str = gap_init; + gap_ext_str = gap_ext; + } + + if(seqs.size()<2){ + reportErr("Input sequences not defined\n"); + } + if(aln_type=='q' && seqs[0].length()>seqs[1].length()){ + reportErr("In semi-global query(1st seq) must be shorter than target(2nd seq)\n"); + } + +} + +void Arguments::printUsage(const char * argv0){ + if(!(strstr(argv0,"RNAmountAlignScan"))){ + printf("\nUsage: %s [options]\n",argv0); + printf("REQUIRED:\n" + "\tRNAmountAlign:\n" + "\t\t-f the input fasta file containing two sequences \n" + "\t\tOR\n" + "\t\t-s provide sequence1 and sequence2\n\n" + + "\nOPTIONS:\n" + + "\nALIGNMENT:\n" + "\t-gi Gap initiation penalty for sequence alignment(Default:-3).\n" + "\t\t\tA negative value should be provided\n\n" + + "\t-ge Gap extension penalty for sequence alignment(Default:-1).\n" + "\t\t\tA negative value should be provided\n\n" + + "\t-gamma Weight of the structural homology. Must be in [0,1](Default:0.5)\n" + "\t\t\tsimilarity = gamma*str_sim + (1-gamma)*seq_sim\n\n" + + "\t-m Similarity matrix file in RIBOSUM format.(Default:RIBOSUM85-60.mat)\n" + "\t\t\tAll RIBOSUM files are included in ./matrices directory\n\n" + + "\t-semi Perform semi-global alignment.\n" + "\t\t\tBoth gap ends of the first sequence will be free of penalty.\n\n" + + "\t-local Perform local alignment\n\n" + + "\t-global Perform global alignment.(Default alignment type)\n\n" + + "\t-alifold Output the consensus structure of the alignment from RNAalifold\n\n" + + "\nSTATISTICS:\n" + "\t\tKA=Karlin-Altschul; EVD=extreme value distribution, ND=normal distribution\n\n" + "\t-stat Report statistics based on the alignment type(Default: off). \n" + "\t\t\tFor local alignments: E-value from Karlin-Altschul or EVD fitting\n" + "\t\t\tFor global alignments: p-value from ND fitting\n" + "\t\t\tFor semi-global alignments: p-value from ND fitting\n\n" + + "\t-evd EVD fitting will be used for local alignments instead of KA\n\n" + + "\t-num Number of random sequences generated for fitting.(Default:500)\n\n" + + "\t-gc Size of GC bins (an integer between [0-100]). (Default: 5)\n" + "\t\t\tThis is used only with with parameter fitting and not KA.\n\n" + + "\nOUTPUT:\n" + "\t-o Write the output to a file.\n" + "\t\t\tIf not used the output will be printed to stdout.\n\n" + + "\t-format Format of the alignment output. (Default: clustal)\n\n" + + "\t-v Verbose output. Prints MFE structures, the ensemble expected and incremental heights.\n\n" + "\t-h Print help\n\n"); + } + else{ + printf("\nUsage: %s [options]\n",argv0); + printf("REQUIRED:\n" + "\tRNAmountAlignScan:\n" + "\t\t-qf fasta file containing query sequence\n" + "\t\tAND\n" + "\t\t-tf fasta file containing target sequence\n\n" + + "\nOPTIONS:\n" + + "\nSLIDING\n" + "\t -window Size of the sliding window(Default:300).\n\n" + + "\t -step Step size for incrementing the window start(Default:200).\n\n" + + + "\nALIGNMENT:\n" + "\t-gi Gap initiation penalty for sequence alignment(Default:-3).\n" + "\t\t\tA negative value should be provided\n\n" + + "\t-ge Gap extension penalty for sequence alignment(Default:-1).\n" + "\t\t\tA negative value should be provided\n\n" + + "\t-gamma Weight of the structural homology. Must be in [0,1](Default:0.5)\n" + "\t\t\tsimilarity = gamma*str_sim + (1-gamma)*seq_sim\n\n" + + "\t-m Similarity matrix file in RIBOSUM format.(Default:RIBOSUM85-60.mat)\n" + "\t\t\tAll RIBOSUM files are included in ./matrices directory\n\n" + + "\t-semi Perform semi-global alignment.\n" + "\t\t\tBoth gap ends of the first sequence will be free of penalty.\n\n" + + "\t-local Perform local alignment\n\n" + + "\t-global Perform global alignment.(Default alignment type)\n\n" + + + "\nSTATISTICS:\n" + "\t\tKA=Karlin-Altschul; EVD=extreme value distribution, ND=normal distribution\n\n" + "\t-stat Report statistics based on the alignment type(Default: off). \n" + "\t\t\tFor local alignments: E-value from Karlin-Altschul(default) or EVD fitting\n" + "\t\t\tFor global alignments: p-value from ND fitting\n" + "\t\t\tFor semi-global alignments: p-value from ND fitting\n\n" + + "\t-evd EVD fitting will be used for local alignments instead of KA\n\n" + + "\t-num Number of random sequences generated for fitting.(Default:500)\n\n" + + "\t-gc Size of GC bins (an integer between [0-100]). (Default: 5)\n" + "\t\t\tThis is used only with with parameter fitting and not KA.\n\n" + + "\nOUTPUT:\n" + "\t-o Write the output to a file.\n" + "\t\t\tIf not used the output will be printed to stdout.\n\n" + + "\t-format Format of the alignment output. (Default: clustal)\n\n" + + "\t-v Verbose output. Prints MFE structures, the ensemble expected and incremental heights.\n\n" + "\t-h Print help\n\n"); + } + + exit(1); +} + +void Arguments::printArgs(){ + string matt(matrix); + printf("#PARAMETERS:\ngap init:%.1f;gap ext:%.1f;structure weight:%.2f\nseq sim matrix=%s\n", + gap_init,gap_ext,str_weight,matt.substr(matt.find_last_of("/\\") + 1).c_str()); + string type=""; + if(aln_type=='l') + type="local"; + else if(aln_type=='g') + type="global"; + else if(aln_type=='q') + type="semi-global"; + printf("Type = %s\n\n",type.c_str()); +} + +string Arguments::sprintArgs(){ + char txt[1000]={0}; + string matt(matrix); + sprintf(txt+strlen(txt),"#PARAMETERS:\ngap init:%.1f; gap ext:%.1f; structure weight:%.2f\nseq sim matrix: %s\n", + gap_init,gap_ext,str_weight,matt.substr(matt.find_last_of("/\\") + 1).c_str()); + string type=""; + if(aln_type=='l') + type="local"; + else if(aln_type=='g') + type="global"; + else if(aln_type=='q') + type="semi-global"; + sprintf(txt+strlen(txt),"Type = %s\n\n",type.c_str()); + return txt; +} + +void Arguments::readFasta(const string fname, vector & seqs, vector & ids){ + ifstream input(fname.c_str()); + if(!input.good()){ + char err[500]; + sprintf(err,"Could not open file %s\n", fname.c_str()); + reportErr(err); + } + vector strs; + string line, name, content,str; + while(getline( input, line ).good() ){ + if( line.empty() || line[0] == '>' ){ + if( !name.empty() ){ + seqs.push_back(content); + if (!str.empty()) + strs.push_back(str); + else + strs.push_back("MFE"); + name.clear(); + } + if( !line.empty() ){ + name = line.substr(1); + ids.push_back(name); + } + content.clear(); + str.clear(); + } else if( !name.empty() ){ + if( line.find(' ') != std::string::npos ){ // Invalid sequence--no spaces allowed + name.clear(); + content.clear(); + } + else if (line[0]=='(' || line[0]==')' || line[0]=='.' ) + str += line; + else + content += line; + } + } + if( !name.empty() ){ // Print out what we read from the last entry + seqs.push_back(content); + if (!str.empty()) + strs.push_back(str); + else + strs.push_back("MFE"); + } + if (seqs.size() >= MAXSEQNUM){ + char err[500]; + sprintf(err,"too much sequences in the fasta file. Maximum is %d\n", MAXSEQNUM); + reportErr(err); + } + return; +} +void Arguments::loadRibosumMatrix(const char * fname){ + string line; + int i,linenum=1; + vector words; + vector nucs; + ifstream file (fname); + if (file.is_open()) + { + while ( getline (file,line) ) + { + istringstream iss(line); + if(linenum == 3){//A C G U + copy(istream_iterator(iss),istream_iterator(),back_inserter(nucs)); + } + else if(3(iss),istream_iterator(),back_inserter(words)); + for(i=1 ; i +#include +#include +#include +#include +#include +#include + +#include "aux.h" + +using namespace std; + +#ifndef ARGUMENTS_H_ +#define ARGUMENTS_H_ + +const int MAXSEQNUM=10000; //maximum number of seqs in fasta file +class Arguments{ +public: + float gap_init; + float gap_ext; + float gap_init_str; + float gap_ext_str; + float str_weight; + int percentile; + bool print_prob; + bool normal; + string eps_name; + string fasta_name; + string query_name; + string target_name; + string output_name; + vector seqs; + vector ids; + char aln_type; + const char * matrix; + float subMat[4][4]; + string outformat; + int window_size; + int step_size; + int rnd_num; + float gc_seg; + bool fixed_gamma; + bool modified_height; + char * exec_path; + bool stats; + bool evd; + bool alifold; + bool qsearch; + char * argv0; + + Arguments(); + void parseArgs(const int argc, char * argv[]); + void printUsage(const char * argv0); + void printArgs(); + string sprintArgs(); + void readFasta(const string fname, vector & seqs, vector & ids); + void loadRibosumMatrix(const char *); +}; + + + + + +#endif /* ARGUMENTS_H_ */ diff --git a/src/aux.cpp b/src/aux.cpp new file mode 100644 index 0000000..20a8447 --- /dev/null +++ b/src/aux.cpp @@ -0,0 +1,354 @@ +#include "aux.h" + +double round_percision(double x,int percision){ + return round(pow(10,percision)*x)/pow(10,percision); +} + +double readBasePairProb(string fname,double pa,double pc,double pg,double pu){ + ifstream infile; + infile.open(fname.c_str()); + double a,c,g,u,op; + if (!infile) reportErr("file %s could not be found!"); + while (infile >> a >> c >> g >> u >> op ) { + if(equal(a,pa) && equal(c,pc) && equal(g,pg) && equal(u,pu)) + break; + } + return op*2.0; +} + +bool equal(double a, double b) +{ + return fabs(a - b) < EPSILON; +} + +void writeVec(char * fname, vector vec){ + ofstream f(fname); + for(vector::iterator it = vec.begin(); it != vec.end(); ++it) + f << *it << '\n'; +} + +float getGCcontent(string seq){ + float gccont=0.0; + for (string::iterator it=seq.begin();it!=seq.end();it++){ + switch(*it){ + case 'C': + case 'G': + case 'c': + case 'g': + gccont+=1; + break; + } + } + //printf("seq:%s ,gc:%f\n",seq.c_str(),gccont/seq.size()); + return (gccont/seq.size()); +} + +vector mergeVectors(vector v1,vector v2){ + vectorv; + v.insert( v.end(), v1.begin(), v1.end() ); + v.insert( v.end(), v2.begin(), v2.end() ); + return v; +} + +double ** allocate2DdoubleArray(int row, int col){ + double ** array = new double * [row]; + for(int i=0; i::max(); + double max=-INF; + if(p>max){ + max = p ; + *ptr = 'P' ; + } + if(q>max){ + max = q ; + *ptr = 'Q' ; + } + if (r>=max){ + max = r ; + *ptr = 'R' ; + } +// printf("%f\t%f\t%f\t%f\t%c\n",p,q,r,max,*ptr); + return max; +} + +void print2Dvec(vector > vec){ + printf("%5c",' '); + for (int j = 0; j < vec[0].size(); ++j) + printf("%5d",j); + printf("\n"); + for (int i = 0; i < vec.size(); ++i){ + printf("%5d",i); + for (int j = 0; j < vec[i].size(); ++j){ + printf("%5.2f",vec[i][j]); + } + printf("\n"); + } +} + + +void printMatrix(vector > mat,int n,int m){ + printf("%5c",' '); + for (int j = 0; j < m; ++j) + printf("%5d",j); + printf("\n"); + for(int i=0;i vec,int percentile){ + int idx = ceil((percentile/100.0) * vec.size()); + return vec.at(max(idx-1,0)); +} + +void reportErr(const char * msg) +{ + cerr << "ERROR: " << msg << "\n"; + exit(EXIT_FAILURE); +} + +void reportWarning(const char * msg) +{ + cerr << "WARNING: " << msg << "\n"; +} + +int char2num(char c){ + int num; + if (c=='A' || c=='a' ) + num=0; + else if(c=='C' || c=='c') + num=1; + else if(c=='G' || c=='g') + num=2; + else if(c=='U' || c=='u' || c=='T' || c=='t') + num=3; + else + reportErr("input sequences should only contain A,C,G,U !"); + return num; +} + +void getNucleotideProbabilities(string seq,vector & nucpr){ + float suma,sumc,sumg,sumu; + suma=sumc=sumg=sumu=0.0; + for(string::iterator it=seq.begin(); it!=seq.end(); ++it){ + switch (*it){ + case 'A': + case 'a': + suma+=1; + break; + case 'C': + case 'c': + sumc+=1; + break; + case 'G': + case 'g': + sumg+=1; + break; + case 'U': + case 'T': + case 't': + case 'u': + sumu+=1; + break; + } + } + nucpr.push_back(suma/seq.size());nucpr.push_back(sumc/seq.size()); + nucpr.push_back(sumg/seq.size());nucpr.push_back(sumu/seq.size()); + //printf("Nucleotide probabilities:%f\t%f\t%f\t%f\n",nucpr[0],nucpr[1],nucpr[2],nucpr[3]); +} + +void generateRandomRNA(char * seq, int length,float pa,float pc,float pg,float pu){ + string NUC = "ACGU"; + float p[4] = {pa,pc,pg,pu}; + for(int i=0;i 0) + { + rnd1 = sre_randseed; + rnd2 = sre_randseed; + /* Fill the table for Bays/Durham */ + for (i = 0; i < 64; i++) { + x = a1*(rnd1%q1); /* LCG1 in action... */ + y = r1*(rnd1/q1); + rnd1 = x-y; + if (rnd1 < 0) rnd1 += m1; + + x = a2*(rnd2%q2); /* LCG2 in action... */ + y = r2*(rnd2/q2); + rnd2 = x-y; + if (rnd2 < 0) rnd2 += m2; + + tbl[i] = rnd1-rnd2; + if (tbl[i] < 0) tbl[i] += m1; + } + sre_randseed = 0; /* drop the flag. */ + }/* end of initialization*/ + + + x = a1*(rnd1%q1); /* LCG1 in action... */ + y = r1*(rnd1/q1); + rnd1 = x-y; + if (rnd1 < 0) rnd1 += m1; + + x = a2*(rnd2%q2); /* LCG2 in action... */ + y = r2*(rnd2/q2); + rnd2 = x-y; + if (rnd2 < 0) rnd2 += m2; + + /* Choose our random number from the table... */ + i = (int) (((double) rnd / (double) m1) * 64.); + rnd = tbl[i]; + /* and replace with a new number by L'Ecuyer. */ + tbl[i] = rnd1-rnd2; + if (tbl[i] < 0) tbl[i] += m1; + + return ((double) rnd / (double) m1); +} + + +char* getExecPath(char* argv0){ + char* exec_path=(char*) malloc (sizeof(char)*PATH_MAX); + exec_path[0]='.'; + exec_path[1]='\0'; + int path_length=1; + FILE* file; + #if defined(_WIN32) + /* GetModuleFileName */ + /* _pgmptr */ + #elif defined(__APPLE__) || defined(__linux) || defined(__unix) || defined(__posix) + char buff[PATH_MAX]; + int bufsize = PATH_MAX-1; + if(file = fopen("/proc/self/exe", "r")){ + fclose(file); + ssize_t len = readlink("/proc/self/exe", buff, bufsize); + if (len != -1) { + buff[len] = '\0'; + strcpy(exec_path, buff); + path_length=len; + } + } + else if(file = fopen("/proc/curproc/file", "r")){ + fclose(file); + ssize_t len = readlink("/proc/curproc/file", buff, bufsize); + if (len != -1) { + buff[len] = '\0'; + strcpy(exec_path, buff); + path_length=len; + } + } + else if(file = fopen("/proc/self/path/a.out", "r")){ + fclose(file); + ssize_t len = readlink("/proc/self/path/a.out", buff, bufsize); + if (len != -1) { + buff[len] = '\0'; + strcpy(exec_path, buff); + path_length=len; + } + } + else{ + strcpy(exec_path, argv0); + } + char* slash_pointer= strrchr(exec_path,'/'); + int slash_position = (int)(slash_pointer - exec_path); + if(slash_position != path_length){ + exec_path[slash_position]='\0'; + } + else{ + exec_path[0]='.'; + exec_path[1]='\0'; + } + + #endif + + + return exec_path; +} + diff --git a/src/aux.h b/src/aux.h new file mode 100644 index 0000000..be84fa1 --- /dev/null +++ b/src/aux.h @@ -0,0 +1,58 @@ +#ifndef AUX_H_ +#define AUX_H_ +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "pair_align.h" + + +using namespace std; +#ifdef _WIN32 + #include +#elif defined(__APPLE__) || defined(__linux) || defined(__unix) || defined(__posix) +#include +#include +#include +#endif + +#define EPSILON 0.0001 +const int LINLEN=60; +extern bool verbose; +double round_percision(double x,int percision); +extern char outtxt[1000000]; +bool equal(double a, double b); +double readBasePairProb(string fname,double pa,double pc,double pg,double pu); +vector mergeVectors(vector v1,vector v2); +double ** allocate2DdoubleArray(int row, int col); +char ** allocate2DcharArray(int row, int col); +void free2DdoubleArray(double ** array,int row); +void free2DcharArray(char ** array,int row); +void free2DAlignmentArray(Alignment **,int); +double max(double p, double q, double r, char * ptr ); +template +void printMatrix0(T ** mat,int n,int m); +void printMatrix(vector > mat,int n,int m); +void printMatrix1(double ** mat,int n,int m); +void printMatrix2(vector > > mat,int n,int m); +void print2Dvec(vector > vec); +double getPercentileFromSortedVector(std::vector vec,int percentile); +char* getExecPath(char* argv0); +void reportErr(const char * msg); +void reportWarning(const char * msg); +int char2num(char); +Alignment ** allocate2DAlignmentArray(int , int ); +void getNucleotideProbabilities(string seq, vector & nucpr); +void generateRandomRNA(char * seq, int length, float pa,float pc,float pg,float pu); +int rouletteWheel(float *p, int n); +double sre_random(); +float getGCcontent(string seq); +void writeVec(char * fname, vector vec); + +#endif /* AUX_H_ */ diff --git a/src/cofold.h b/src/cofold.h new file mode 100755 index 0000000..048a65c --- /dev/null +++ b/src/cofold.h @@ -0,0 +1,182 @@ +#ifndef __VIENNA_RNA_PACKAGE_COFOLD_H__ +#define __VIENNA_RNA_PACKAGE_COFOLD_H__ + +#include "data_structures.h" + +#ifdef __GNUC__ +#define DEPRECATED(func) func __attribute__ ((deprecated)) +#else +#define DEPRECATED(func) func +#endif + +/** + * \addtogroup cofold + * \brief Predict structures formed by two molecules upon hybridization. + * + * The function of an RNA molecule often depends on its interaction with + * other RNAs. The following routines therefore allow to predict structures + * formed by two RNA molecules upon hybridization.\n + * One approach to co-folding two RNAs consists of concatenating the two + * sequences and keeping track of the concatenation point in all energy + * evaluations. Correspondingly, many of the cofold() and + * co_pf_fold() routines below take one sequence string as argument + * and use the the global variable #cut_point to mark the concatenation + * point. Note that while the RNAcofold program uses the '&' character + * to mark the chain break in its input, you should not use an '&' when using + * the library routines (set #cut_point instead).\n + * In a second approach to co-folding two RNAs, cofolding is seen as a + * stepwise process. In the first step the probability of an unpaired region + * is calculated and in a second step this probability of an unpaired region + * is multiplied with the probability of an interaction between the two RNAs. + * This approach is implemented for the interaction between a long + * target sequence and a short ligand RNA. Function pf_unstru() calculates + * the partition function over all unpaired regions in the input + * sequence. Function pf_interact(), which calculates the + * partition function over all possible interactions between two + * sequences, needs both sequence as separate strings as input. + * + */ + +/** + * \addtogroup mfe_cofold + * @{ + * \file cofold.h + * + * \brief MFE version of cofolding routines + * + * This file includes (almost) all function declarations within the RNAlib that are related to + * MFE Cofolding... + * This also includes the Zuker suboptimals calculations, since they are implemented using the cofold + * routines. + */ + +/** + * \brief Compute the minimum free energy of two interacting RNA molecules + * + * The code is analog to the fold() function. If #cut_point ==-1 results + * should be the same as with fold(). + * + * \ingroup mfe_cofold + * + * \param sequence The two sequences concatenated + * \param structure Will hold the barcket dot structure of the dimer molecule + * \return minimum free energy of the structure + */ +float cofold( const char *sequence, + char *structure); + +/** + * \brief Compute the minimum free energy of two interacting RNA molecules + * + */ +float cofold_par( const char *string, + char *structure, + paramT *parameters, + int is_constrained); + +/** + * \brief Free memory occupied by cofold() + */ +void free_co_arrays(void); + +/** + * \brief Recalculate parameters + */ +void update_cofold_params(void); + +void update_cofold_params_par(paramT *parameters); + + +/** + * \brief Export the arrays of partition function cofold (with gquadruplex support) + * + * Export the cofold arrays for use e.g. in the concentration + * Computations or suboptimal secondary structure backtracking + * + * \param f5_p A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j] + * \param c_p A pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j + * \param fML_p A pointer to the 'M' array, i.e. array containing best free energy in interval [i,j] for any multiloop segment with at least one stem + * \param fM1_p A pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem + * \param fc_p A pointer to the 'fc' array, i.e. array ... + * \param ggg_p A pointer to the 'ggg' array, i.e. array containing best free energy of a gquadruplex delimited by [i,j] + * \param indx_p A pointer to the indexing array used for accessing the energy matrices + * \param ptype_p A pointer to the ptype array containing the base pair types for each possibility (i,j) + */ +void export_cofold_arrays_gq( int **f5_p, + int **c_p, + int **fML_p, + int **fM1_p, + int **fc_p, + int **ggg_p, + int **indx_p, + char **ptype_p); + +/** + * \brief Export the arrays of partition function cofold + * + * Export the cofold arrays for use e.g. in the concentration + * Computations or suboptimal secondary structure backtracking + * + * \param f5_p A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j] + * \param c_p A pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j + * \param fML_p A pointer to the 'M' array, i.e. array containing best free energy in interval [i,j] for any multiloop segment with at least one stem + * \param fM1_p A pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem + * \param fc_p A pointer to the 'fc' array, i.e. array ... + * \param indx_p A pointer to the indexing array used for accessing the energy matrices + * \param ptype_p A pointer to the ptype array containing the base pair types for each possibility (i,j) + */ +void export_cofold_arrays(int **f5_p, + int **c_p, + int **fML_p, + int **fM1_p, + int **fc_p, + int **indx_p, + char **ptype_p); + + +/** + * @} + */ + +/** + * \brief Compute Zuker type suboptimal structures + * + * Compute Suboptimal structures according to M. Zuker, i.e. for every + * possible base pair the minimum energy structure containing the resp. base pair. + * Returns a list of these structures and their energies. + * + * \ingroup subopt_zuker + * + * \param string RNA sequence + * \return List of zuker suboptimal structures + */ +SOLUTION *zukersubopt(const char *string); + +/** + * \brief Compute Zuker type suboptimal structures + * + * \ingroup subopt_zuker + * + */ +SOLUTION *zukersubopt_par( const char *string, + paramT *parameters); + +/** + * \brief get_monomer_free_energies + * + * Export monomer free energies out of cofold arrays + * + * \param e1 A pointer to a variable where the energy of molecule A will be written to + * \param e2 A pointer to a variable where the energy of molecule B will be written to + */ +void get_monomere_mfes( float *e1, + float *e2); + + +/** + * allocate arrays for folding + * \deprecated{This function is obsolete and will be removed soon!} + */ +DEPRECATED(void initialize_cofold(int length)); + +#endif diff --git a/src/data_structures.h b/src/data_structures.h new file mode 100644 index 0000000..52a2e7b --- /dev/null +++ b/src/data_structures.h @@ -0,0 +1,775 @@ +#ifndef __VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H__ +#define __VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H__ + +#include "energy_const.h" +/** + * \file data_structures.h + * \brief All datastructures and typedefs shared among the Vienna RNA Package can be found here + */ + +/* to use floats instead of doubles in pf_fold() comment next line */ +#define LARGE_PF +#ifdef LARGE_PF +#define FLT_OR_DBL double +#else +#define FLT_OR_DBL float +#endif + +#ifndef NBASES +#define NBASES 8 +#endif + +#ifndef MAXALPHA +/** + * \brief Maximal length of alphabet + */ +#define MAXALPHA 20 +#endif + +/** + * \brief Maximum density of states discretization for subopt + */ +#define MAXDOS 1000 + +#define VRNA_GQUAD_MAX_STACK_SIZE 7 +#define VRNA_GQUAD_MIN_STACK_SIZE 2 +#define VRNA_GQUAD_MAX_LINKER_LENGTH 15 +#define VRNA_GQUAD_MIN_LINKER_LENGTH 1 +#define VRNA_GQUAD_MIN_BOX_SIZE ((4*VRNA_GQUAD_MIN_STACK_SIZE)+(3*VRNA_GQUAD_MIN_LINKER_LENGTH)) +#define VRNA_GQUAD_MAX_BOX_SIZE ((4*VRNA_GQUAD_MAX_STACK_SIZE)+(3*VRNA_GQUAD_MAX_LINKER_LENGTH)) + + +/* +* ############################################################ +* Here are the type definitions of various datastructures +* shared among the Vienna RNA Package +* ############################################################ +*/ + +/** + * \brief this datastructure is used as input parameter in functions of PS_dot.h and others + */ +typedef struct plist { + int i; + int j; + float p; + int type; +} plist; + +/** + * \brief this datastructure is used as input parameter in functions of PS_dot.c + */ +typedef struct cpair { + int i,j,mfe; + float p, hue, sat; +} cpair; + +/** + * \brief this is a workarround for the SWIG Perl Wrapper RNA plot function + * that returns an array of type COORDINATE + */ +typedef struct { + float X; /* X coords */ + float Y; /* Y coords */ +} COORDINATE; + +/** + * \brief Stack of partial structures for backtracking + */ +typedef struct sect { + int i; + int j; + int ml; +} sect; + +/** + * \brief Base pair + */ +typedef struct bondT { + unsigned int i; + unsigned int j; +} bondT; + +/** + * \brief Base pair with associated energy + */ +typedef struct bondTEn { + int i; + int j; + int energy; +} bondTEn; + +/** + * \brief The data structure that contains the complete model details used throughout the calculations + * + */ +typedef struct{ + int dangles; /**< \brief Specifies the dangle model used in any energy evaluation (0,1,2 or 3) + \note Some function do not implement all dangle model but only a subset of + (0,1,2,3). Read the documentaion of the particular recurrences or + energy evaluation function for information about the provided dangle + model. + */ + int special_hp; /**< \brief Include special hairpin contributions for tri, tetra and hexaloops */ + int noLP; /**< \brief Only consider canonical structures, i.e. no 'lonely' base pairs */ + int noGU; /**< \brief Do not allow GU pairs */ + int noGUclosure; /**< \brief Do not allow loops to be closed by GU pair */ + int logML; /**< \brief Use logarithmic scaling for multi loops */ + int circ; /**< \brief Assume molecule to be circular */ + int gquad; /**< \brief Include G-quadruplexes in structure prediction */ + int canonicalBPonly; /**< \brief remove non-canonical bp's from constraint structures */ +} model_detailsT; + +/** + * \brief The datastructure that contains temperature scaled energy parameters. + */ +typedef struct{ + int id; + int stack[NBPAIRS+1][NBPAIRS+1]; + int hairpin[31]; + int bulge[MAXLOOP+1]; + int internal_loop[MAXLOOP+1]; + int mismatchExt[NBPAIRS+1][5][5]; + int mismatchI[NBPAIRS+1][5][5]; + int mismatch1nI[NBPAIRS+1][5][5]; + int mismatch23I[NBPAIRS+1][5][5]; + int mismatchH[NBPAIRS+1][5][5]; + int mismatchM[NBPAIRS+1][5][5]; + int dangle5[NBPAIRS+1][5]; + int dangle3[NBPAIRS+1][5]; + int int11[NBPAIRS+1][NBPAIRS+1][5][5]; + int int21[NBPAIRS+1][NBPAIRS+1][5][5][5]; + int int22[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; + int ninio[5]; + double lxc; + int MLbase; + int MLintern[NBPAIRS+1]; + int MLclosing; + int TerminalAU; + int DuplexInit; + int Tetraloop_E[200]; + char Tetraloops[1401]; + int Triloop_E[40]; + char Triloops[241]; + int Hexaloop_E[40]; + char Hexaloops[1801]; + int TripleC; + int MultipleCA; + int MultipleCB; + int gquad [VRNA_GQUAD_MAX_STACK_SIZE + 1] + [3*VRNA_GQUAD_MAX_LINKER_LENGTH + 1]; + + double temperature; /**< \brief Temperature used for loop contribution scaling */ + + model_detailsT model_details; /**< \brief Model details to be used in the recursions */ + +} paramT; + +/** + * \brief The datastructure that contains temperature scaled Boltzmann weights of the energy parameters. + */ +typedef struct{ + int id; + double expstack[NBPAIRS+1][NBPAIRS+1]; + double exphairpin[31]; + double expbulge[MAXLOOP+1]; + double expinternal[MAXLOOP+1]; + double expmismatchExt[NBPAIRS+1][5][5]; + double expmismatchI[NBPAIRS+1][5][5]; + double expmismatch23I[NBPAIRS+1][5][5]; + double expmismatch1nI[NBPAIRS+1][5][5]; + double expmismatchH[NBPAIRS+1][5][5]; + double expmismatchM[NBPAIRS+1][5][5]; + double expdangle5[NBPAIRS+1][5]; + double expdangle3[NBPAIRS+1][5]; + double expint11[NBPAIRS+1][NBPAIRS+1][5][5]; + double expint21[NBPAIRS+1][NBPAIRS+1][5][5][5]; + double expint22[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; + double expninio[5][MAXLOOP+1]; + double lxc; + double expMLbase; + double expMLintern[NBPAIRS+1]; + double expMLclosing; + double expTermAU; + double expDuplexInit; + double exptetra[40]; + double exptri[40]; + double exphex[40]; + char Tetraloops[1401]; + double expTriloop[40]; + char Triloops[241]; + char Hexaloops[1801]; + double expTripleC; + double expMultipleCA; + double expMultipleCB; + double expgquad[VRNA_GQUAD_MAX_STACK_SIZE + 1] + [3*VRNA_GQUAD_MAX_LINKER_LENGTH + 1]; + + double kT; + double pf_scale; /**< \brief Scaling factor to avoid over-/underflows */ + + double temperature; /**< \brief Temperature used for loop contribution scaling */ + double alpha; /**< \brief Scaling factor for the thermodynamic temperature + \details This allows for temperature scaling in Boltzmann + factors independently from the energy contributions. + The resulting Boltzmann factors are then computed by + \f$ e^{-E/(\alpha \cdot K \cdot T)} \f$ + */ + + model_detailsT model_details; /**< \brief Model details to be used in the recursions */ + +} pf_paramT; + + + +/* +* ############################################################ +* SUBOPT data structures +* ############################################################ +*/ + + +/** + * \brief Base pair data structure used in subopt.c + */ +typedef struct { + int i; + int j; +} PAIR; + +/** + * \brief Sequence interval stack element used in subopt.c + */ +typedef struct { + int i; + int j; + int array_flag; +} INTERVAL; + +/** + * \brief Solution element from subopt.c + */ +typedef struct { + float energy; /**< \brief Free Energy of structure in kcal/mol */ + char *structure; /**< \brief Structure in dot-bracket notation */ +} SOLUTION; + +/* +* ############################################################ +* COFOLD data structures +* ############################################################ +*/ + +/** + * \brief + */ +typedef struct cofoldF { + /* free energies for: */ + double F0AB; /**< \brief Null model without DuplexInit */ + double FAB; /**< \brief all states with DuplexInit correction */ + double FcAB; /**< \brief true hybrid states only */ + double FA; /**< \brief monomer A */ + double FB; /**< \brief monomer B */ +} cofoldF; + +/** + * \brief + */ +typedef struct ConcEnt { + double A0; /**< \brief start concentration A */ + double B0; /**< \brief start concentration B */ + double ABc; /**< \brief End concentration AB */ + double AAc; + double BBc; + double Ac; + double Bc; +} ConcEnt; + +/** + * \brief + */ +typedef struct pairpro{ + struct plist *AB; + struct plist *AA; + struct plist *A; + struct plist *B; + struct plist *BB; +}pairpro; + +/** + * \brief A base pair info structure + * + * For each base pair (i,j) with i,j in [0, n-1] the structure lists: + * - its probability 'p' + * - an entropy-like measure for its well-definedness 'ent' + * - the frequency of each type of pair in 'bp[]' + * + 'bp[0]' contains the number of non-compatible sequences + * + 'bp[1]' the number of CG pairs, etc. + */ +typedef struct { + unsigned i; /**< \brief nucleotide position i */ + unsigned j; /**< \brief nucleotide position j */ + float p; /**< \brief Probability */ + float ent; /**< \brief Pseudo entropy for \f$ p(i,j) = S_i + S_j - p_ij*ln(p_ij) \f$ */ + short bp[8]; /**< \brief Frequencies of pair_types */ + char comp; /**< \brief 1 iff pair is in mfe structure */ +} pair_info; + + +/* +* ############################################################ +* FINDPATH data structures +* ############################################################ +*/ + +/** + * \brief + */ +typedef struct move { + int i; /* i,j>0 insert; i,j<0 delete */ + int j; + int when; /* 0 if still available, else resulting distance from start */ + int E; +} move_t; + +/** + * \brief + */ +typedef struct intermediate { + short *pt; /**< \brief pair table */ + int Sen; /**< \brief saddle energy so far */ + int curr_en; /**< \brief current energy */ + move_t *moves; /**< \brief remaining moves to target */ +} intermediate_t; + +/** + * \brief + */ +typedef struct path { + double en; + char *s; +} path_t; + +/* +* ############################################################ +* RNAup data structures +* ############################################################ +*/ + +/** + * \brief contributions to p_u + */ +typedef struct pu_contrib { + double **H; /**< \brief hairpin loops */ + double **I; /**< \brief interior loops */ + double **M; /**< \brief multi loops */ + double **E; /**< \brief exterior loop */ + int length; /**< \brief length of the input sequence */ + int w; /**< \brief longest unpaired region */ +} pu_contrib; + +/** + * \brief + */ +typedef struct interact { + double *Pi; /**< \brief probabilities of interaction */ + double *Gi; /**< \brief free energies of interaction */ + double Gikjl; /**< \brief full free energy for interaction between [k,i] k (k_max, l_max) */ + int *E_F5_rem; + int *E_F3_rem; + int *E_C_rem; + int *E_M_rem; + int *E_M1_rem; + int *E_M2_rem; + + int E_Fc_rem; + int E_FcH_rem; + int E_FcI_rem; + int E_FcM_rem; + +#ifdef COUNT_STATES + unsigned long ***N_F5; + unsigned long ***N_C; + unsigned long ***N_M; + unsigned long ***N_M1; +#endif +} TwoDfold_vars; + +/** + * \brief Solution element returned from TwoDpfoldList + * + * This element contains the partition function for the appropriate + * kappa (k), lambda (l) neighborhood + * The datastructure contains two integer attributes 'k' and 'l' + * as well as an attribute 'q' of type #FLT_OR_DBL + * + * A value of #INF in k denotes the end of a list + * + * \see TwoDpfoldList() + */ +typedef struct{ + int k; /**< \brief Distance to first reference */ + int l; /**< \brief Distance to second reference */ + FLT_OR_DBL q; /**< \brief partition function */ +} TwoDpfold_solution; + +/** + * \brief Variables compound for 2Dfold partition function folding + * + * \see get_TwoDpfold_variables(), get_TwoDpfold_variables_from_MFE(), + * destroy_TwoDpfold_variables(), TwoDpfoldList() + */ +typedef struct{ + + unsigned int alloc; + char *ptype; /**< \brief Precomputed array of pair types */ + char *sequence; /**< \brief The input sequence */ + short *S, *S1; /**< \brief The input sequences in numeric form */ + unsigned int maxD1; /**< \brief Maximum allowed base pair distance to first reference */ + unsigned int maxD2; /**< \brief Maximum allowed base pair distance to second reference */ + + double temperature; /* temperature in last call to scale_pf_params */ + double init_temp; /* temperature in last call to scale_pf_params */ + FLT_OR_DBL *scale; + FLT_OR_DBL pf_scale; + pf_paramT *pf_params; /* holds all [unscaled] pf parameters */ + + int *my_iindx; /**< \brief Index for moving in quadratic distancy dimensions */ + int *jindx; /**< \brief Index for moving in the triangular matrix qm1 */ + + short *reference_pt1; + short *reference_pt2; + + unsigned int *referenceBPs1; /**< \brief Matrix containing number of basepairs of reference structure1 in interval [i,j] */ + unsigned int *referenceBPs2; /**< \brief Matrix containing number of basepairs of reference structure2 in interval [i,j] */ + unsigned int *bpdist; /**< \brief Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j] */ + + unsigned int *mm1; /**< \brief Maximum matching matrix, reference struct 1 disallowed */ + unsigned int *mm2; /**< \brief Maximum matching matrix, reference struct 2 disallowed */ + + int circ; + int dangles; + unsigned int seq_length; + + FLT_OR_DBL ***Q; + FLT_OR_DBL ***Q_B; + FLT_OR_DBL ***Q_M; + FLT_OR_DBL ***Q_M1; + FLT_OR_DBL ***Q_M2; + + FLT_OR_DBL **Q_c; + FLT_OR_DBL **Q_cH; + FLT_OR_DBL **Q_cI; + FLT_OR_DBL **Q_cM; + + int **l_min_values; + int **l_max_values; + int *k_min_values; + int *k_max_values; + + int **l_min_values_b; + int **l_max_values_b; + int *k_min_values_b; + int *k_max_values_b; + + int **l_min_values_m; + int **l_max_values_m; + int *k_min_values_m; + int *k_max_values_m; + + int **l_min_values_m1; + int **l_max_values_m1; + int *k_min_values_m1; + int *k_max_values_m1; + + int **l_min_values_m2; + int **l_max_values_m2; + int *k_min_values_m2; + int *k_max_values_m2; + + int *l_min_values_qc; + int *l_max_values_qc; + int k_min_values_qc; + int k_max_values_qc; + + int *l_min_values_qcH; + int *l_max_values_qcH; + int k_min_values_qcH; + int k_max_values_qcH; + + int *l_min_values_qcI; + int *l_max_values_qcI; + int k_min_values_qcI; + int k_max_values_qcI; + + int *l_min_values_qcM; + int *l_max_values_qcM; + int k_min_values_qcM; + int k_max_values_qcM; + + /* auxilary arrays for remaining set of coarse graining (k,l) > (k_max, l_max) */ + FLT_OR_DBL *Q_rem; + FLT_OR_DBL *Q_B_rem; + FLT_OR_DBL *Q_M_rem; + FLT_OR_DBL *Q_M1_rem; + FLT_OR_DBL *Q_M2_rem; + + FLT_OR_DBL Q_c_rem; + FLT_OR_DBL Q_cH_rem; + FLT_OR_DBL Q_cI_rem; + FLT_OR_DBL Q_cM_rem; + +} TwoDpfold_vars; + +#endif diff --git a/src/energy_const.h b/src/energy_const.h new file mode 100644 index 0000000..e677f58 --- /dev/null +++ b/src/energy_const.h @@ -0,0 +1,33 @@ +#ifndef __VIENNA_RNA_PACKAGE_ENERGY_CONST_H__ +#define __VIENNA_RNA_PACKAGE_ENERGY_CONST_H__ + +#include + +/** + * \file energy_const.h + * energy constants + */ + +/** The gas constant */ +#define GASCONST 1.98717 /* in [cal/K] */ +/** 0 deg Celsius in Kelvin */ +#define K0 273.15 +/** Infinity as used in minimization routines */ +#define INF 10000000 /* (INT_MAX/10) */ + +#define EMAX (INF/10) +/** forbidden */ +#define FORBIDDEN 9999 +/** bonus contribution */ +#define BONUS 10000 +/** The number of distinguishable base pairs */ +#define NBPAIRS 7 +/** The minimum loop length */ +#define TURN 3 +/** The maximum loop length */ +#define MAXLOOP 30 + +#define VRNA_GQUAD_MISMATCH_PENALTY 300 /* penalty for incompatible nucleotides in an alignment that destruct a gquad layer */ +#define VRNA_GQUAD_MISMATCH_NUM_ALI 1 /* maximum number of mismatching sequences in the alignment when gquad should be formed */ + +#endif diff --git a/src/energy_params/rna_andronescu2007.par b/src/energy_params/rna_andronescu2007.par new file mode 100644 index 0000000..c810a3a --- /dev/null +++ b/src/energy_params/rna_andronescu2007.par @@ -0,0 +1,9899 @@ +## RNAfold parameter file v2.0 + +# stack +/* CG GC GU UG AU UA @ */ + -203 -271 -178 -85 -199 -178 0 + -271 -300 -193 -127 -189 -211 0 + -178 -193 30 -71 -88 -47 0 + -85 -127 -71 -70 -1 0 0 + -199 -189 -88 -1 -99 -69 0 + -178 -211 -47 0 -69 -91 0 + 0 0 0 0 0 0 0 + +# stack_enthalpies +/* CG GC GU UG AU UA @ */ + -1060 -1340 -1210 -560 -1050 -1040 0 + -1340 -1490 -1260 -830 -1140 -1240 0 + -1210 -1260 -1460 -1350 -880 -1280 0 + -560 -830 -1350 -930 -320 -700 0 + -1050 -1140 -880 -320 -940 -680 0 + -1040 -1240 -1280 -700 -680 -770 0 + 0 0 0 0 0 0 0 + +# mismatch_hairpin + 0 0 0 0 0 + -90 -161 -156 -118 -85 + -90 -115 -167 -301 -120 + -90 -185 -119 -172 -202 + -90 -209 -150 -280 -218 + 0 0 0 0 0 + -70 -150 -197 -230 -110 + -70 -180 -170 -174 -150 + -70 -181 -190 -188 -178 + -70 -90 -155 -239 -229 + 0 0 0 0 0 + 0 -80 50 70 70 + 0 -57 -4 -80 -9 + 0 -187 -210 -130 100 + 0 -130 -56 60 -120 + 0 0 0 0 0 + 0 -68 -130 -160 -148 + 0 80 -110 -121 -100 + 0 -128 -220 -130 -170 + 0 12 -110 -160 -149 + 0 0 0 0 0 + 0 -77 -150 -119 -37 + 0 -110 -120 -250 -68 + 0 -210 -58 -107 9 + 0 -130 70 -119 -157 + 0 0 0 0 0 + 0 -74 -125 -125 50 + 0 8 -110 -133 -69 + 0 -154 -220 -144 59 + 0 -130 -72 -149 -106 + 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 + +# mismatch_hairpin_enthalpies + 0 0 0 0 0 + DEF -1030 -950 -1030 -1030 + DEF -520 -450 -520 -670 + DEF -940 -940 -940 -940 + DEF -810 -740 -810 -860 + 0 0 0 0 0 + DEF -520 -880 -560 -880 + DEF -720 -310 -310 -390 + DEF -710 -740 -620 -740 + DEF -500 -500 -500 -570 + 0 0 0 0 0 + DEF -430 -600 -600 -600 + DEF -260 -240 -240 -240 + DEF -340 -690 -690 -690 + DEF -330 -330 -330 -330 + 0 0 0 0 0 + DEF -720 -790 -960 -810 + DEF -480 -480 -360 -480 + DEF -660 -810 -920 -810 + DEF -550 -440 -550 -360 + 0 0 0 0 0 + DEF -430 -600 -600 -600 + DEF -260 -240 -240 -240 + DEF -340 -690 -690 -690 + DEF -330 -330 -330 -330 + 0 0 0 0 0 + DEF -400 -630 -890 -590 + DEF -430 -510 -200 -180 + DEF -380 -680 -890 -680 + DEF -280 -140 -280 -140 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + +# mismatch_interior + 0 0 0 0 0 + 0 0 0 -76 0 + 0 0 0 0 0 + 0 -76 0 0 0 + 0 0 0 0 -68 + 0 0 0 0 0 + 0 0 0 -76 0 + 0 0 0 0 0 + 0 -76 0 0 0 + 0 0 0 0 -68 + 0 0 0 0 0 + 0 66 66 -10 66 + 0 66 66 66 66 + 0 -10 66 66 66 + 0 66 66 66 -2 + 0 0 0 0 0 + 0 66 66 -10 66 + 0 66 66 66 66 + 0 -10 66 66 66 + 0 66 66 66 -2 + 0 0 0 0 0 + 0 66 66 -10 66 + 0 66 66 66 66 + 0 -10 66 66 66 + 0 66 66 66 -2 + 0 0 0 0 0 + 0 66 66 -10 66 + 0 66 66 66 66 + 0 -10 66 66 66 + 0 66 66 66 -2 + 90 90 90 90 90 + 90 90 90 90 -20 + 90 90 90 90 90 + 90 -20 90 90 90 + 90 90 90 90 20 + +# mismatch_interior_enthalpies + 0 0 0 0 0 + DEF -1030 -950 -1030 -1030 + DEF -520 -450 -520 -670 + DEF -940 -940 -940 -940 + DEF -810 -740 -810 -860 + 0 0 0 0 0 + DEF -520 -880 -560 -880 + DEF -720 -310 -310 -390 + DEF -710 -740 -620 -740 + DEF -500 -500 -500 -570 + 0 0 0 0 0 + DEF -430 -600 -600 -600 + DEF -260 -240 -240 -240 + DEF -340 -690 -690 -690 + DEF -330 -330 -330 -330 + 0 0 0 0 0 + DEF -720 -790 -960 -810 + DEF -480 -480 -360 -480 + DEF -660 -810 -920 -810 + DEF -550 -440 -550 -360 + 0 0 0 0 0 + DEF -430 -600 -600 -600 + DEF -260 -240 -240 -240 + DEF -340 -690 -690 -690 + DEF -330 -330 -330 -330 + 0 0 0 0 0 + DEF -400 -630 -890 -590 + DEF -430 -510 -200 -180 + DEF -380 -680 -890 -680 + DEF -280 -140 -280 -140 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + +# mismatch_interior_1n + 0 0 0 0 0 + 0 0 0 -76 0 + 0 0 0 0 0 + 0 -76 0 0 0 + 0 0 0 0 -68 + 0 0 0 0 0 + 0 0 0 -76 0 + 0 0 0 0 0 + 0 -76 0 0 0 + 0 0 0 0 -68 + 0 0 0 0 0 + 0 66 66 -10 66 + 0 66 66 66 66 + 0 -10 66 66 66 + 0 66 66 66 -2 + 0 0 0 0 0 + 0 66 66 -10 66 + 0 66 66 66 66 + 0 -10 66 66 66 + 0 66 66 66 -2 + 0 0 0 0 0 + 0 66 66 -10 66 + 0 66 66 66 66 + 0 -10 66 66 66 + 0 66 66 66 -2 + 0 0 0 0 0 + 0 66 66 -10 66 + 0 66 66 66 66 + 0 -10 66 66 66 + 0 66 66 66 -2 + 90 90 90 90 90 + 90 90 90 90 -20 + 90 90 90 90 90 + 90 -20 90 90 90 + 90 90 90 90 20 + +# mismatch_interior_1n_enthalpies + 0 0 0 0 0 + DEF -1030 -950 -1030 -1030 + DEF -520 -450 -520 -670 + DEF -940 -940 -940 -940 + DEF -810 -740 -810 -860 + 0 0 0 0 0 + DEF -520 -880 -560 -880 + DEF -720 -310 -310 -390 + DEF -710 -740 -620 -740 + DEF -500 -500 -500 -570 + 0 0 0 0 0 + DEF -430 -600 -600 -600 + DEF -260 -240 -240 -240 + DEF -340 -690 -690 -690 + DEF -330 -330 -330 -330 + 0 0 0 0 0 + DEF -720 -790 -960 -810 + DEF -480 -480 -360 -480 + DEF -660 -810 -920 -810 + DEF -550 -440 -550 -360 + 0 0 0 0 0 + DEF -430 -600 -600 -600 + DEF -260 -240 -240 -240 + DEF -340 -690 -690 -690 + DEF -330 -330 -330 -330 + 0 0 0 0 0 + DEF -400 -630 -890 -590 + DEF -430 -510 -200 -180 + DEF -380 -680 -890 -680 + DEF -280 -140 -280 -140 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + +# mismatch_interior_23 + 0 0 0 0 0 + 0 0 0 -76 0 + 0 0 0 0 0 + 0 -76 0 0 0 + 0 0 0 0 -68 + 0 0 0 0 0 + 0 0 0 -76 0 + 0 0 0 0 0 + 0 -76 0 0 0 + 0 0 0 0 -68 + 0 0 0 0 0 + 0 66 66 -10 66 + 0 66 66 66 66 + 0 -10 66 66 66 + 0 66 66 66 -2 + 0 0 0 0 0 + 0 66 66 -10 66 + 0 66 66 66 66 + 0 -10 66 66 66 + 0 66 66 66 -2 + 0 0 0 0 0 + 0 66 66 -10 66 + 0 66 66 66 66 + 0 -10 66 66 66 + 0 66 66 66 -2 + 0 0 0 0 0 + 0 66 66 -10 66 + 0 66 66 66 66 + 0 -10 66 66 66 + 0 66 66 66 -2 + 90 90 90 90 90 + 90 90 90 90 -20 + 90 90 90 90 90 + 90 -20 90 90 90 + 90 90 90 90 20 + +# mismatch_interior_23_enthalpies + 0 0 0 0 0 + DEF -1030 -950 -1030 -1030 + DEF -520 -450 -520 -670 + DEF -940 -940 -940 -940 + DEF -810 -740 -810 -860 + 0 0 0 0 0 + DEF -520 -880 -560 -880 + DEF -720 -310 -310 -390 + DEF -710 -740 -620 -740 + DEF -500 -500 -500 -570 + 0 0 0 0 0 + DEF -430 -600 -600 -600 + DEF -260 -240 -240 -240 + DEF -340 -690 -690 -690 + DEF -330 -330 -330 -330 + 0 0 0 0 0 + DEF -720 -790 -960 -810 + DEF -480 -480 -360 -480 + DEF -660 -810 -920 -810 + DEF -550 -440 -550 -360 + 0 0 0 0 0 + DEF -430 -600 -600 -600 + DEF -260 -240 -240 -240 + DEF -340 -690 -690 -690 + DEF -330 -330 -330 -330 + 0 0 0 0 0 + DEF -400 -630 -890 -590 + DEF -430 -510 -200 -180 + DEF -380 -680 -890 -680 + DEF -280 -140 -280 -140 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + +# mismatch_multi +/* @ A C G U */ + 0 -73 -124 -159 -152 + -17 -90 -141 -176 -169 + -55 -128 -179 -214 -207 + -32 -105 -156 -191 -184 + -23 -96 -147 -182 -175 + 0 -139 -55 -152 -161 + -17 -156 -72 -169 -178 + -55 -194 -110 -207 -216 + -32 -171 -87 -184 -193 + -23 -162 -78 -175 -184 + 0 -17 -55 -32 -23 + 0 -17 -55 -32 -23 + 0 -17 -55 -32 -23 + 0 -17 -55 -32 -23 + -23 -40 -78 -55 -46 + 0 -17 -55 -180 -23 + 0 -17 -55 -180 -23 + -55 -72 -110 -235 -78 + 0 -17 -55 -180 -23 + 0 -17 -55 -180 -23 + 0 -17 -55 -96 -23 + -10 -27 -65 -106 -33 + 0 -17 -55 -96 -23 + -3 -20 -58 -99 -26 + -23 -40 -78 -119 -46 + 0 -17 -55 -94 -23 + -17 -34 -72 -111 -40 + -55 -72 -110 -149 -78 + 0 -17 -55 -94 -23 + -23 -40 -78 -117 -46 + 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 + +# mismatch_multi_enthalpies +/* @ A C G U */ + 0 -740 -280 -640 -360 + -240 -980 -520 -880 -600 + 330 -410 50 -310 -30 + 80 -660 -200 -560 -280 + -140 -880 -420 -780 -500 + 0 -900 -410 -860 -750 + -160 -1060 -570 -1020 -910 + 70 -830 -340 -790 -680 + -460 -1360 -870 -1320 -1210 + -40 -940 -450 -900 -790 + 0 -740 -240 -720 -490 + 160 -580 -80 -560 -330 + 220 -520 -20 -500 -270 + 70 -670 -170 -650 -420 + 310 -430 70 -410 -180 + 0 -490 -90 -550 -230 + -150 -640 -240 -700 -380 + 510 20 420 -40 280 + 10 -480 -80 -540 -220 + 100 -390 10 -450 -130 + 0 -570 -70 -580 -220 + 160 -410 90 -420 -60 + 220 -350 150 -360 0 + 70 -500 0 -510 -150 + 310 -260 240 -270 90 + 0 -490 -90 -550 -230 + DEF -540 -140 -600 -280 + 690 200 600 140 460 + -60 -550 -150 -610 -290 + -60 -550 -150 -610 -290 + 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 + +# mismatch_exterior +/* @ A C G U */ + 0 -73 -124 -159 -152 + -17 -90 -141 -176 -169 + -55 -128 -179 -214 -207 + -32 -105 -156 -191 -184 + -23 -96 -147 -182 -175 + 0 -139 -55 -152 -161 + -17 -156 -72 -169 -178 + -55 -194 -110 -207 -216 + -32 -171 -87 -184 -193 + -23 -162 -78 -175 -184 + 0 -17 -55 -32 -23 + 0 -17 -55 -32 -23 + 0 -17 -55 -32 -23 + 0 -17 -55 -32 -23 + -23 -40 -78 -55 -46 + 0 -17 -55 -180 -23 + 0 -17 -55 -180 -23 + -55 -72 -110 -235 -78 + 0 -17 -55 -180 -23 + 0 -17 -55 -180 -23 + 0 -17 -55 -96 -23 + -10 -27 -65 -106 -33 + 0 -17 -55 -96 -23 + -3 -20 -58 -99 -26 + -23 -40 -78 -119 -46 + 0 -17 -55 -94 -23 + -17 -34 -72 -111 -40 + -55 -72 -110 -149 -78 + 0 -17 -55 -94 -23 + -23 -40 -78 -117 -46 + 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 + +# mismatch_exterior_enthalpies +/* @ A C G U */ + 0 -740 -280 -640 -360 + -240 -980 -520 -880 -600 + 330 -410 50 -310 -30 + 80 -660 -200 -560 -280 + -140 -880 -420 -780 -500 + 0 -900 -410 -860 -750 + -160 -1060 -570 -1020 -910 + 70 -830 -340 -790 -680 + -460 -1360 -870 -1320 -1210 + -40 -940 -450 -900 -790 + 0 -740 -240 -720 -490 + 160 -580 -80 -560 -330 + 220 -520 -20 -500 -270 + 70 -670 -170 -650 -420 + 310 -430 70 -410 -180 + 0 -490 -90 -550 -230 + -150 -640 -240 -700 -380 + 510 20 420 -40 280 + 10 -480 -80 -540 -220 + 100 -390 10 -450 -130 + 0 -570 -70 -580 -220 + 160 -410 90 -420 -60 + 220 -350 150 -360 0 + 70 -500 0 -510 -150 + 310 -260 240 -270 90 + 0 -490 -90 -550 -230 + DEF -540 -140 -600 -280 + 690 200 600 140 460 + -60 -550 -150 -610 -290 + -60 -550 -150 -610 -290 + 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 + +# dangle5 +/* @ A C G U */ + INF -17 -55 -32 -23 + INF -17 -55 -32 -23 + INF 0 0 0 -23 + INF 0 -55 0 0 + INF -10 0 -3 -23 + INF -17 -55 0 -23 + 0 0 0 0 0 + +# dangle5_enthalpies +/* @ A C G U */ + 0 -240 330 80 -140 + 0 -160 70 -460 -40 + 0 160 220 70 310 + 0 -150 510 10 100 + 0 160 220 70 310 + 0 DEF 690 -60 -60 + 0 0 0 0 0 + +# dangle3 +/* @ A C G U */ + INF -73 -124 -159 -152 + INF -139 -55 -152 -161 + INF -17 -55 -32 -23 + INF -17 -55 -180 -23 + INF -17 -55 -96 -23 + INF -17 -55 -94 -23 + 0 0 0 0 0 + +# dangle3_enthalpies +/* @ A C G U */ + 0 -740 -280 -640 -360 + 0 -900 -410 -860 -750 + 0 -740 -240 -720 -490 + 0 -490 -90 -550 -230 + 0 -570 -70 -580 -220 + 0 -490 -90 -550 -230 + 0 0 0 0 0 + +# int11 +/* CG..CG */ + 210 210 210 210 210 + 210 166 3 137 -4 + 210 3 70 -4 2 + 210 137 -4 -40 -4 + 210 -4 2 -4 20 +/* CG..GC */ + 210 210 210 210 210 + 210 108 58 19 -4 + 210 70 50 -4 70 + 210 16 -4 -70 -4 + 210 -4 14 -4 13 +/* CG..GU */ + 210 210 210 210 210 + 210 62 62 62 62 + 210 62 62 62 62 + 210 62 62 -4 62 + 210 62 62 62 62 +/* CG..UG */ + 210 210 210 210 210 + 210 62 62 62 62 + 210 62 62 62 62 + 210 62 62 -4 62 + 210 62 62 62 62 +/* CG..AU */ + 210 210 210 210 210 + 210 62 62 62 62 + 210 62 62 62 62 + 210 62 62 -4 62 + 210 62 62 62 210 +/* CG..UA */ + 210 210 210 210 210 + 210 62 62 62 62 + 210 62 62 62 62 + 210 62 62 -4 62 + 210 62 62 62 134 +/* CG.. @ */ + 210 210 210 210 210 + 210 210 210 210 210 + 210 210 210 210 210 + 210 210 210 210 210 + 210 210 210 210 210 +/* GC..CG */ + 210 210 210 210 210 + 210 108 70 16 -4 + 210 58 50 -4 14 + 210 19 -4 -70 -4 + 210 -4 70 -4 13 +/* GC..GC */ + 210 210 210 210 210 + 210 -2 -60 -60 -4 + 210 -60 82 -4 -60 + 210 -60 -4 -195 -4 + 210 -4 -60 -4 -169 +/* GC..GU */ + 210 210 210 210 210 + 210 62 62 62 62 + 210 62 62 62 62 + 210 62 62 -4 62 + 210 62 62 62 62 +/* GC..UG */ + 210 210 210 210 210 + 210 62 62 62 62 + 210 62 62 62 62 + 210 62 62 -4 62 + 210 62 62 62 62 +/* GC..AU */ + 210 210 210 210 210 + 210 62 62 62 62 + 210 62 62 62 62 + 210 62 62 -4 62 + 210 62 62 62 15 +/* GC..UA */ + 210 210 210 210 210 + 210 62 62 62 62 + 210 62 62 62 62 + 210 62 62 -4 62 + 210 62 62 62 98 +/* GC.. @ */ + 210 210 210 210 210 + 210 210 210 210 210 + 210 210 210 210 210 + 210 210 210 210 210 + 210 210 210 210 210 +/* GU..CG */ + 210 210 210 210 210 + 210 62 62 62 62 + 210 62 62 62 62 + 210 62 62 -4 62 + 210 62 62 62 62 +/* GU..GC */ + 210 210 210 210 210 + 210 62 62 62 62 + 210 62 62 62 62 + 210 62 62 -4 62 + 210 62 62 62 62 +/* GU..GU */ + 137 137 137 137 137 + 137 128 128 128 128 + 137 128 128 128 128 + 137 128 128 62 128 + 137 128 128 128 128 +/* GU..UG */ + 137 137 137 137 137 + 137 128 128 128 128 + 137 128 128 128 128 + 137 128 128 62 128 + 137 128 128 128 128 +/* GU..AU */ + 137 137 137 137 137 + 137 128 128 128 128 + 137 128 128 128 128 + 137 128 128 62 128 + 137 128 128 128 128 +/* GU..UA */ + 137 137 137 137 137 + 137 128 128 128 128 + 137 128 128 128 128 + 137 128 128 62 128 + 137 128 128 128 128 +/* GU.. @ */ + 137 137 137 137 137 + 137 137 137 137 137 + 137 137 137 137 137 + 137 137 137 137 137 + 137 137 137 137 137 +/* UG..CG */ + 210 210 210 210 210 + 210 62 62 62 62 + 210 62 62 62 62 + 210 62 62 -4 62 + 210 62 62 62 62 +/* UG..GC */ + 210 210 210 210 210 + 210 62 62 62 62 + 210 62 62 62 62 + 210 62 62 -4 62 + 210 62 62 62 62 +/* UG..GU */ + 137 137 137 137 137 + 137 128 128 128 128 + 137 128 128 128 128 + 137 128 128 62 128 + 137 128 128 128 128 +/* UG..UG */ + 137 137 137 137 137 + 137 128 128 128 128 + 137 128 128 128 128 + 137 128 128 62 128 + 137 128 128 128 128 +/* UG..AU */ + 137 137 137 137 137 + 137 128 128 128 128 + 137 128 128 128 128 + 137 128 128 62 128 + 137 128 128 128 128 +/* UG..UA */ + 137 137 137 137 137 + 137 128 128 128 128 + 137 128 128 128 128 + 137 128 128 62 128 + 137 128 128 128 128 +/* UG.. @ */ + 137 137 137 137 137 + 137 137 137 137 137 + 137 137 137 137 137 + 137 137 137 137 137 + 137 137 137 137 137 +/* AU..CG */ + 210 210 210 210 210 + 210 62 62 62 62 + 210 62 62 62 62 + 210 62 62 -4 62 + 210 62 62 62 210 +/* AU..GC */ + 210 210 210 210 210 + 210 62 62 62 62 + 210 62 62 62 62 + 210 62 62 -4 62 + 210 62 62 62 15 +/* AU..GU */ + 137 137 137 137 137 + 137 128 128 128 128 + 137 128 128 128 128 + 137 128 128 62 128 + 137 128 128 128 128 +/* AU..UG */ + 137 137 137 137 137 + 137 128 128 128 128 + 137 128 128 128 128 + 137 128 128 62 128 + 137 128 128 128 128 +/* AU..AU */ + 137 137 137 137 137 + 137 128 128 128 128 + 137 128 128 128 128 + 137 128 128 62 128 + 137 128 128 128 137 +/* AU..UA */ + 137 137 137 137 137 + 137 128 128 128 128 + 137 128 128 128 128 + 137 128 128 62 128 + 137 128 128 128 128 +/* AU.. @ */ + 137 137 137 137 137 + 137 137 137 137 137 + 137 137 137 137 137 + 137 137 137 137 137 + 137 137 137 137 137 +/* UA..CG */ + 210 210 210 210 210 + 210 62 62 62 62 + 210 62 62 62 62 + 210 62 62 -4 62 + 210 62 62 62 134 +/* UA..GC */ + 210 210 210 210 210 + 210 62 62 62 62 + 210 62 62 62 62 + 210 62 62 -4 62 + 210 62 62 62 98 +/* UA..GU */ + 137 137 137 137 137 + 137 128 128 128 128 + 137 128 128 128 128 + 137 128 128 62 128 + 137 128 128 128 128 +/* UA..UG */ + 137 137 137 137 137 + 137 128 128 128 128 + 137 128 128 128 128 + 137 128 128 62 128 + 137 128 128 128 128 +/* UA..AU */ + 137 137 137 137 137 + 137 128 128 128 128 + 137 128 128 128 128 + 137 128 128 62 128 + 137 128 128 128 128 +/* UA..UA */ + 137 137 137 137 137 + 137 128 128 128 128 + 137 128 128 128 128 + 137 128 128 62 128 + 137 128 128 128 123 +/* UA.. @ */ + 137 137 137 137 137 + 137 137 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486 +/* GC.@..CG */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* GC.A..CG */ + 486 486 486 486 486 + 486 216 204 233 400 + 486 175 270 260 400 + 486 124 160 29 400 + 486 400 400 400 400 +/* GC.C..CG */ + 486 486 486 486 486 + 486 130 320 400 320 + 486 320 150 400 320 + 486 400 400 400 400 + 486 282 290 400 214 +/* GC.G..CG */ + 486 486 486 486 486 + 486 158 400 90 400 + 486 400 400 400 400 + 486 180 400 120 400 + 486 400 400 400 400 +/* GC.U..CG */ + 486 486 486 486 486 + 486 400 400 400 400 + 486 400 320 400 220 + 486 400 400 400 400 + 486 400 251 400 220 +/* GC.@..GC */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* GC.A..GC */ + 486 486 486 486 486 + 486 221 162 184 400 + 486 142 191 260 400 + 486 112 160 84 400 + 486 400 400 400 400 +/* GC.C..GC */ + 486 486 486 486 486 + 486 130 270 400 320 + 486 222 165 400 278 + 486 400 400 400 400 + 486 229 211 400 267 +/* GC.G..GC */ + 486 486 486 486 486 + 486 115 400 50 400 + 486 400 400 400 400 + 486 122 400 220 400 + 486 400 400 400 400 +/* GC.U..GC */ + 486 486 486 486 486 + 486 400 400 400 400 + 486 400 241 400 175 + 486 400 400 400 400 + 486 400 160 400 154 +/* GC.@..GU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* GC.A..GU */ + 486 486 486 486 486 + 486 264 205 227 443 + 486 185 234 303 443 + 486 155 203 127 443 + 486 443 443 443 443 +/* GC.C..GU */ + 486 486 486 486 486 + 486 173 313 443 363 + 486 265 208 443 321 + 486 443 443 443 443 + 486 272 254 443 310 +/* GC.G..GU */ + 486 486 486 486 486 + 486 158 443 93 443 + 486 443 443 443 443 + 486 165 443 263 443 + 486 443 443 443 443 +/* GC.U..GU */ + 486 486 486 486 486 + 486 443 443 443 443 + 486 443 284 443 218 + 486 443 443 443 443 + 486 443 203 443 197 +/* GC.@..UG */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* GC.A..UG */ + 486 486 486 486 486 + 486 264 205 227 443 + 486 185 234 303 443 + 486 155 203 127 443 + 486 443 443 443 443 +/* GC.C..UG */ + 486 486 486 486 486 + 486 173 313 443 363 + 486 265 208 443 321 + 486 443 443 443 443 + 486 272 254 443 310 +/* GC.G..UG */ + 486 486 486 486 486 + 486 158 443 93 443 + 486 443 443 443 443 + 486 165 443 263 443 + 486 443 443 443 443 +/* GC.U..UG */ + 486 486 486 486 486 + 486 443 443 443 443 + 486 443 284 443 218 + 486 443 443 443 443 + 486 443 203 443 197 +/* GC.@..AU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* GC.A..AU */ + 486 486 486 486 486 + 486 264 205 227 443 + 486 185 234 303 443 + 486 155 203 127 443 + 486 443 443 443 443 +/* GC.C..AU */ + 486 486 486 486 486 + 486 173 313 443 363 + 486 265 208 443 321 + 486 443 443 443 443 + 486 272 254 443 310 +/* GC.G..AU */ + 486 486 486 486 486 + 486 158 443 93 443 + 486 443 443 443 443 + 486 165 443 263 443 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443 443 443 443 + 486 443 203 443 197 +/* GU.@..GC */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* GU.A..GC */ + 486 486 486 486 486 + 486 264 205 227 443 + 486 185 234 303 443 + 486 155 203 127 443 + 486 443 443 443 443 +/* GU.C..GC */ + 486 486 486 486 486 + 486 173 313 443 363 + 486 265 208 443 321 + 486 443 443 443 443 + 486 272 254 443 310 +/* GU.G..GC */ + 486 486 486 486 486 + 486 158 443 93 443 + 486 443 443 443 443 + 486 165 443 263 443 + 486 443 443 443 443 +/* GU.U..GC */ + 486 486 486 486 486 + 486 443 443 443 443 + 486 443 284 443 218 + 486 443 443 443 443 + 486 443 203 443 197 +/* GU.@..GU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* GU.A..GU */ + 486 486 486 486 486 + 486 307 248 270 486 + 486 228 277 346 486 + 486 198 246 170 486 + 486 486 486 486 486 +/* GU.C..GU */ + 486 486 486 486 486 + 486 216 356 486 406 + 486 308 251 486 364 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443 + 486 185 234 303 443 + 486 155 203 127 443 + 486 443 443 443 443 +/* UG.C..CG */ + 486 486 486 486 486 + 486 173 313 443 363 + 486 265 208 443 321 + 486 443 443 443 443 + 486 272 254 443 310 +/* UG.G..CG */ + 486 486 486 486 486 + 486 158 443 93 443 + 486 443 443 443 443 + 486 165 443 263 443 + 486 443 443 443 443 +/* UG.U..CG */ + 486 486 486 486 486 + 486 443 443 443 443 + 486 443 284 443 218 + 486 443 443 443 443 + 486 443 203 443 197 +/* UG.@..GC */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* UG.A..GC */ + 486 486 486 486 486 + 486 264 205 227 443 + 486 185 234 303 443 + 486 155 203 127 443 + 486 443 443 443 443 +/* UG.C..GC */ + 486 486 486 486 486 + 486 173 313 443 363 + 486 265 208 443 321 + 486 443 443 443 443 + 486 272 254 443 310 +/* UG.G..GC */ + 486 486 486 486 486 + 486 158 443 93 443 + 486 443 443 443 443 + 486 165 443 263 443 + 486 443 443 443 443 +/* UG.U..GC */ + 486 486 486 486 486 + 486 443 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486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* UG.A..UA */ + 486 486 486 486 486 + 486 307 248 270 486 + 486 228 277 346 486 + 486 198 246 170 486 + 486 486 486 486 486 +/* UG.C..UA */ + 486 486 486 486 486 + 486 216 356 486 406 + 486 308 251 486 364 + 486 486 486 486 486 + 486 315 297 486 353 +/* UG.G..UA */ + 486 486 486 486 486 + 486 201 486 136 486 + 486 486 486 486 486 + 486 208 486 306 486 + 486 486 486 486 486 +/* UG.U..UA */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 327 486 261 + 486 486 486 486 486 + 486 486 246 486 240 +/* UG.@.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* UG.A.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* UG.C.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* UG.G.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* UG.U.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* AU.@..CG */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* AU.A..CG */ + 486 486 486 486 486 + 486 264 205 227 443 + 486 185 234 303 443 + 486 155 203 127 443 + 486 443 443 443 443 +/* AU.C..CG */ + 486 486 486 486 486 + 486 173 313 443 363 + 486 265 208 443 321 + 486 443 443 443 443 + 486 272 254 443 310 +/* AU.G..CG */ + 486 486 486 486 486 + 486 158 443 93 443 + 486 443 443 443 443 + 486 165 443 263 443 + 486 443 443 443 443 +/* AU.U..CG */ + 486 486 486 486 486 + 486 443 443 443 443 + 486 443 284 443 218 + 486 443 443 443 443 + 486 443 203 443 197 +/* AU.@..GC */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* AU.A..GC */ + 486 486 486 486 486 + 486 264 205 227 443 + 486 185 234 303 443 + 486 155 203 127 443 + 486 443 443 443 443 +/* AU.C..GC */ + 486 486 486 486 486 + 486 173 313 443 363 + 486 265 208 443 321 + 486 443 443 443 443 + 486 272 254 443 310 +/* AU.G..GC */ + 486 486 486 486 486 + 486 158 443 93 443 + 486 443 443 443 443 + 486 165 443 263 443 + 486 443 443 443 443 +/* AU.U..GC */ + 486 486 486 486 486 + 486 443 443 443 443 + 486 443 284 443 218 + 486 443 443 443 443 + 486 443 203 443 197 +/* AU.@..GU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* AU.A..GU */ + 486 486 486 486 486 + 486 307 248 270 486 + 486 228 277 346 486 + 486 198 246 170 486 + 486 486 486 486 486 +/* AU.C..GU */ + 486 486 486 486 486 + 486 216 356 486 406 + 486 308 251 486 364 + 486 486 486 486 486 + 486 315 297 486 353 +/* AU.G..GU */ + 486 486 486 486 486 + 486 201 486 136 486 + 486 486 486 486 486 + 486 208 486 306 486 + 486 486 486 486 486 +/* AU.U..GU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 327 486 261 + 486 486 486 486 486 + 486 486 246 486 240 +/* AU.@..UG */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* AU.A..UG */ + 486 486 486 486 486 + 486 307 248 270 486 + 486 228 277 346 486 + 486 198 246 170 486 + 486 486 486 486 486 +/* AU.C..UG */ + 486 486 486 486 486 + 486 216 356 486 406 + 486 308 251 486 364 + 486 486 486 486 486 + 486 315 297 486 353 +/* AU.G..UG */ + 486 486 486 486 486 + 486 201 486 136 486 + 486 486 486 486 486 + 486 208 486 306 486 + 486 486 486 486 486 +/* AU.U..UG */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 327 486 261 + 486 486 486 486 486 + 486 486 246 486 240 +/* AU.@..AU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* AU.A..AU */ + 486 486 486 486 486 + 486 307 248 270 486 + 486 228 277 346 486 + 486 198 246 170 486 + 486 486 486 486 486 +/* AU.C..AU */ + 486 486 486 486 486 + 486 216 356 486 406 + 486 308 251 486 364 + 486 486 486 486 486 + 486 315 297 486 353 +/* AU.G..AU */ + 486 486 486 486 486 + 486 201 486 136 486 + 486 486 486 486 486 + 486 208 486 306 486 + 486 486 486 486 486 +/* AU.U..AU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 327 486 261 + 486 486 486 486 486 + 486 486 246 486 240 +/* AU.@..UA */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* AU.A..UA */ + 486 486 486 486 486 + 486 307 248 270 486 + 486 228 277 346 486 + 486 198 246 170 486 + 486 486 486 486 486 +/* AU.C..UA */ + 486 486 486 486 486 + 486 216 356 486 406 + 486 308 251 486 364 + 486 486 486 486 486 + 486 315 297 486 353 +/* AU.G..UA */ + 486 486 486 486 486 + 486 201 486 136 486 + 486 486 486 486 486 + 486 208 486 306 486 + 486 486 486 486 486 +/* AU.U..UA */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 327 486 261 + 486 486 486 486 486 + 486 486 246 486 240 +/* AU.@.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* AU.A.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* AU.C.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* AU.G.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* AU.U.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* UA.@..CG */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* UA.A..CG */ + 486 486 486 486 486 + 486 264 205 227 443 + 486 185 234 303 443 + 486 155 203 127 443 + 486 443 443 443 443 +/* UA.C..CG */ + 486 486 486 486 486 + 486 173 313 443 363 + 486 265 208 443 321 + 486 443 443 443 443 + 486 272 254 443 310 +/* UA.G..CG */ + 486 486 486 486 486 + 486 158 443 93 443 + 486 443 443 443 443 + 486 165 443 263 443 + 486 443 443 443 443 +/* UA.U..CG */ + 486 486 486 486 486 + 486 443 443 443 443 + 486 443 284 443 218 + 486 443 443 443 443 + 486 443 203 443 197 +/* UA.@..GC */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* UA.A..GC */ + 486 486 486 486 486 + 486 264 205 227 443 + 486 185 234 303 443 + 486 155 203 127 443 + 486 443 443 443 443 +/* UA.C..GC */ + 486 486 486 486 486 + 486 173 313 443 363 + 486 265 208 443 321 + 486 443 443 443 443 + 486 272 254 443 310 +/* UA.G..GC */ + 486 486 486 486 486 + 486 158 443 93 443 + 486 443 443 443 443 + 486 165 443 263 443 + 486 443 443 443 443 +/* UA.U..GC */ + 486 486 486 486 486 + 486 443 443 443 443 + 486 443 284 443 218 + 486 443 443 443 443 + 486 443 203 443 197 +/* UA.@..GU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* UA.A..GU */ + 486 486 486 486 486 + 486 307 248 270 486 + 486 228 277 346 486 + 486 198 246 170 486 + 486 486 486 486 486 +/* UA.C..GU */ + 486 486 486 486 486 + 486 216 356 486 406 + 486 308 251 486 364 + 486 486 486 486 486 + 486 315 297 486 353 +/* UA.G..GU */ + 486 486 486 486 486 + 486 201 486 136 486 + 486 486 486 486 486 + 486 208 486 306 486 + 486 486 486 486 486 +/* UA.U..GU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 327 486 261 + 486 486 486 486 486 + 486 486 246 486 240 +/* UA.@..UG */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* UA.A..UG */ + 486 486 486 486 486 + 486 307 248 270 486 + 486 228 277 346 486 + 486 198 246 170 486 + 486 486 486 486 486 +/* UA.C..UG */ + 486 486 486 486 486 + 486 216 356 486 406 + 486 308 251 486 364 + 486 486 486 486 486 + 486 315 297 486 353 +/* UA.G..UG */ + 486 486 486 486 486 + 486 201 486 136 486 + 486 486 486 486 486 + 486 208 486 306 486 + 486 486 486 486 486 +/* UA.U..UG */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 327 486 261 + 486 486 486 486 486 + 486 486 246 486 240 +/* UA.@..AU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* UA.A..AU */ + 486 486 486 486 486 + 486 307 248 270 486 + 486 228 277 346 486 + 486 198 246 170 486 + 486 486 486 486 486 +/* UA.C..AU */ + 486 486 486 486 486 + 486 216 356 486 406 + 486 308 251 486 364 + 486 486 486 486 486 + 486 315 297 486 353 +/* UA.G..AU */ + 486 486 486 486 486 + 486 201 486 136 486 + 486 486 486 486 486 + 486 208 486 306 486 + 486 486 486 486 486 +/* UA.U..AU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 327 486 261 + 486 486 486 486 486 + 486 486 246 486 240 +/* UA.@..UA */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* UA.A..UA */ + 486 486 486 486 486 + 486 307 248 270 486 + 486 228 277 346 486 + 486 198 246 170 486 + 486 486 486 486 486 +/* UA.C..UA */ + 486 486 486 486 486 + 486 216 356 486 406 + 486 308 251 486 364 + 486 486 486 486 486 + 486 315 297 486 353 +/* UA.G..UA */ + 486 486 486 486 486 + 486 201 486 136 486 + 486 486 486 486 486 + 486 208 486 306 486 + 486 486 486 486 486 +/* UA.U..UA */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 327 486 261 + 486 486 486 486 486 + 486 486 246 486 240 +/* UA.@.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* UA.A.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* UA.C.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* UA.G.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* UA.U.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.@..CG */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.A..CG */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.C..CG */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.G..CG */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.U..CG */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.@..GC */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.A..GC */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.C..GC */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.G..GC */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.U..GC */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.@..GU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.A..GU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.C..GU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.G..GU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.U..GU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.@..UG */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.A..UG */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.C..UG */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.G..UG */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.U..UG */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.@..AU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.A..AU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.C..AU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.G..AU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.U..AU */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.@..UA */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.A..UA */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.C..UA */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.G..UA */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.U..UA */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.@.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.A.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.C.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.G.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 +/* @.U.. @ */ + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + 486 486 486 486 486 + +# int21_enthalpies +/* CG.@..CG */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* CG.A..CG */ + DEF -1029 -949 -1029 -1029 + -1079 -2058 -1978 -2058 -2058 + -569 -1548 -1468 -1548 -1548 + -989 -1968 -1888 -1968 -1968 + -859 -1838 -1758 -1838 -1838 +/* CG.C..CG */ + DEF -519 -449 -519 -669 + -999 -1468 -1398 -1468 -1618 + -499 -968 -898 -968 -1118 + -989 -1458 -1388 -1458 -1608 + -789 -1258 -1188 -1258 -1408 +/* CG.G..CG */ + DEF -939 -939 -939 -939 + -1079 -1968 -1968 -1968 -1968 + -569 -1458 -1458 -1458 -1458 + -989 -1878 -1878 -1878 -1878 + -859 -1748 -1748 -1748 -1748 +/* CG.U..CG */ + DEF -809 -739 -809 -859 + -1079 -1838 -1768 -1838 -1888 + -719 -1478 -1408 -1478 -1528 + -989 -1748 -1678 -1748 -1798 + -909 -1668 -1598 -1668 -1718 +/* CG.@..GC */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* CG.A..GC */ + DEF -1029 -949 -1029 -1029 + -569 -1548 -1468 -1548 -1548 + -769 -1748 -1668 -1748 -1748 + -759 -1738 -1658 -1738 -1738 + -549 -1528 -1448 -1528 -1528 +/* CG.C..GC */ + DEF -519 -449 -519 -669 + -929 -1398 -1328 -1398 -1548 + -359 -828 -758 -828 -978 + -789 -1258 -1188 -1258 -1408 + -549 -1018 -948 -1018 -1168 +/* CG.G..GC */ + DEF -939 -939 -939 -939 + -609 -1498 -1498 -1498 -1498 + -359 -1248 -1248 -1248 -1248 + -669 -1558 -1558 -1558 -1558 + -549 -1438 -1438 -1438 -1438 +/* CG.U..GC */ + DEF -809 -739 -809 -859 + -929 -1688 -1618 -1688 -1738 + -439 -1198 -1128 -1198 -1248 + -789 -1548 -1478 -1548 -1598 + -619 -1378 -1308 -1378 -1428 +/* CG.@..GU */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* CG.A..GU */ + DEF -1029 -949 -1029 -1029 + -479 -1458 -1378 -1458 -1458 + -309 -1288 -1208 -1288 -1288 + -389 -1368 -1288 -1368 -1368 + -379 -1358 -1278 -1358 -1358 +/* CG.C..GU */ + DEF -519 -449 -519 -669 + -649 -1118 -1048 -1118 -1268 + -289 -758 -688 -758 -908 + -739 -1208 -1138 -1208 -1358 + -379 -848 -778 -848 -998 +/* CG.G..GU */ + DEF -939 -939 -939 -939 + -649 -1538 -1538 -1538 -1538 + -289 -1178 -1178 -1178 -1178 + -739 -1628 -1628 -1628 -1628 + -379 -1268 -1268 -1268 -1268 +/* CG.U..GU */ + DEF -809 -739 -809 -859 + -649 -1408 -1338 -1408 -1458 + -289 -1048 -978 -1048 -1098 + -739 -1498 -1428 -1498 -1548 + -379 -1138 -1068 -1138 -1188 +/* CG.@..UG */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* CG.A..UG */ + DEF -1029 -949 -1029 -1029 + -769 -1748 -1668 -1748 -1748 + -529 -1508 -1428 -1508 -1508 + -709 -1688 -1608 -1688 -1688 + -599 -1578 -1498 -1578 -1578 +/* CG.C..UG */ + DEF -519 -449 -519 -669 + -839 -1308 -1238 -1308 -1458 + -529 -998 -928 -998 -1148 + -859 -1328 -1258 -1328 -1478 + -489 -958 -888 -958 -1108 +/* CG.G..UG */ + DEF -939 -939 -939 -939 + -1009 -1898 -1898 -1898 -1898 + -409 -1298 -1298 -1298 -1298 + -969 -1858 -1858 -1858 -1858 + -599 -1488 -1488 -1488 -1488 +/* CG.U..UG */ + DEF -809 -739 -809 -859 + -859 -1618 -1548 -1618 -1668 + -529 -1288 -1218 -1288 -1338 + -859 -1618 -1548 -1618 -1668 + -409 -1168 -1098 -1168 -1218 +/* CG.@..AU */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* CG.A..AU */ + DEF -1029 -949 -1029 -1029 + -479 -1458 -1378 -1458 -1458 + -309 -1288 -1208 -1288 -1288 + -389 -1368 -1288 -1368 -1368 + -379 -1358 -1278 -1358 -1358 +/* CG.C..AU */ + DEF -519 -449 -519 -669 + -649 -1118 -1048 -1118 -1268 + -289 -758 -688 -758 -908 + -739 -1208 -1138 -1208 -1358 + -379 -848 -778 -848 -998 +/* CG.G..AU */ + DEF -939 -939 -939 -939 + -649 -1538 -1538 -1538 -1538 + -289 -1178 -1178 -1178 -1178 + -739 -1628 -1628 -1628 -1628 + -379 -1268 -1268 -1268 -1268 +/* CG.U..AU */ + DEF -809 -739 -809 -859 + -649 -1408 -1338 -1408 -1458 + -289 -1048 -978 -1048 -1098 + -739 -1498 -1428 -1498 -1548 + -379 -1138 -1068 -1138 -1188 +/* CG.@..UA */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* CG.A..UA */ + DEF -1029 -949 -1029 -1029 + -449 -1428 -1348 -1428 -1428 + -479 -1458 -1378 -1458 -1458 + -429 -1408 -1328 -1408 -1408 + -329 -1308 -1228 -1308 -1308 +/* CG.C..UA */ + DEF -519 -449 -519 -669 + -679 -1148 -1078 -1148 -1298 + -559 -1028 -958 -1028 -1178 + -729 -1198 -1128 -1198 -1348 + -189 -658 -588 -658 -808 +/* CG.G..UA */ + DEF -939 -939 -939 -939 + -939 -1828 -1828 -1828 -1828 + -249 -1138 -1138 -1138 -1138 + -939 -1828 -1828 -1828 -1828 + -329 -1218 -1218 -1218 -1218 +/* CG.U..UA */ + DEF -809 -739 -809 -859 + -639 -1398 -1328 -1398 -1448 + -229 -988 -918 -988 -1038 + -729 -1488 -1418 -1488 -1538 + -190 -949 -879 -949 -999 +/* CG.@.. @ */ + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* CG.A.. @ */ + -100 -1079 -999 -1079 -1079 + -100 -1079 -999 -1079 -1079 + -100 -1079 -999 -1079 -1079 + -100 -1079 -999 -1079 -1079 + -100 -1079 -999 -1079 -1079 +/* CG.C.. @ */ + -100 -569 -499 -569 -719 + -100 -569 -499 -569 -719 + -100 -569 -499 -569 -719 + -100 -569 -499 -569 -719 + -100 -569 -499 -569 -719 +/* CG.G.. @ */ + -100 -989 -989 -989 -989 + -100 -989 -989 -989 -989 + -100 -989 -989 -989 -989 + -100 -989 -989 -989 -989 + -100 -989 -989 -989 -989 +/* CG.U.. @ */ + -100 -859 -789 -859 -909 + -100 -859 -789 -859 -909 + -100 -859 -789 -859 -909 + -100 -859 -789 -859 -909 + -100 -859 -789 -859 -909 +/* GC.@..CG */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* GC.A..CG */ + DEF -519 -879 -559 -879 + -1079 -1548 -1908 -1588 -1908 + -569 -1038 -1398 -1078 -1398 + -989 -1458 -1818 -1498 -1818 + -859 -1328 -1688 -1368 -1688 +/* GC.C..CG */ + DEF -719 -309 -309 -389 + -999 -1668 -1258 -1258 -1338 + -499 -1168 -758 -758 -838 + -989 -1658 -1248 -1248 -1328 + -789 -1458 -1048 -1048 -1128 +/* GC.G..CG */ + DEF -709 -739 -619 -739 + -1079 -1738 -1768 -1648 -1768 + -569 -1228 -1258 -1138 -1258 + -989 -1648 -1678 -1558 -1678 + -859 -1518 -1548 -1428 -1548 +/* GC.U..CG */ + DEF -499 -499 -499 -569 + -1079 -1528 -1528 -1528 -1598 + -719 -1168 -1168 -1168 -1238 + -989 -1438 -1438 -1438 -1508 + -909 -1358 -1358 -1358 -1428 +/* GC.@..GC */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* GC.A..GC */ + DEF -519 -879 -559 -879 + -569 -1038 -1398 -1078 -1398 + -769 -1238 -1598 -1278 -1598 + -759 -1228 -1588 -1268 -1588 + -549 -1018 -1378 -1058 -1378 +/* GC.C..GC */ + DEF -719 -309 -309 -389 + -929 -1598 -1188 -1188 -1268 + 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DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* UG.A.. @ */ + -100 -769 -839 -1009 -859 + -100 -769 -839 -1009 -859 + -100 -769 -839 -1009 -859 + -100 -769 -839 -1009 -859 + -100 -769 -839 -1009 -859 +/* UG.C.. @ */ + -100 -529 -529 -409 -529 + -100 -529 -529 -409 -529 + -100 -529 -529 -409 -529 + -100 -529 -529 -409 -529 + -100 -529 -529 -409 -529 +/* UG.G.. @ */ + -100 -709 -859 -969 -859 + -100 -709 -859 -969 -859 + -100 -709 -859 -969 -859 + -100 -709 -859 -969 -859 + -100 -709 -859 -969 -859 +/* UG.U.. @ */ + -100 -599 -489 -599 -409 + -100 -599 -489 -599 -409 + -100 -599 -489 -599 -409 + -100 -599 -489 -599 -409 + -100 -599 -489 -599 -409 +/* AU.@..CG */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* AU.A..CG */ + DEF -429 -599 -599 -599 + -1079 -1458 -1628 -1628 -1628 + -569 -948 -1118 -1118 -1118 + -989 -1368 -1538 -1538 -1538 + -859 -1238 -1408 -1408 -1408 +/* AU.C..CG */ + DEF -259 -239 -239 -239 + -999 -1208 -1188 -1188 -1188 + -499 -708 -688 -688 -688 + -989 -1198 -1178 -1178 -1178 + -789 -998 -978 -978 -978 +/* AU.G..CG */ + DEF -339 -689 -689 -689 + -1079 -1368 -1718 -1718 -1718 + -569 -858 -1208 -1208 -1208 + -989 -1278 -1628 -1628 -1628 + -859 -1148 -1498 -1498 -1498 +/* AU.U..CG */ + DEF -329 -329 -329 -329 + -1079 -1358 -1358 -1358 -1358 + -719 -998 -998 -998 -998 + -989 -1268 -1268 -1268 -1268 + -909 -1188 -1188 -1188 -1188 +/* AU.@..GC */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* AU.A..GC */ + DEF -429 -599 -599 -599 + -569 -948 -1118 -1118 -1118 + -769 -1148 -1318 -1318 -1318 + -759 -1138 -1308 -1308 -1308 + -549 -928 -1098 -1098 -1098 +/* AU.C..GC */ + DEF -259 -239 -239 -239 + -929 -1138 -1118 -1118 -1118 + -359 -568 -548 -548 -548 + -789 -998 -978 -978 -978 + -549 -758 -738 -738 -738 +/* AU.G..GC */ + DEF -339 -689 -689 -689 + -609 -898 -1248 -1248 -1248 + -359 -648 -998 -998 -998 + -669 -958 -1308 -1308 -1308 + -549 -838 -1188 -1188 -1188 +/* AU.U..GC */ + DEF -329 -329 -329 -329 + -929 -1208 -1208 -1208 -1208 + -439 -718 -718 -718 -718 + -789 -1068 -1068 -1068 -1068 + -619 -898 -898 -898 -898 +/* AU.@..GU */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* AU.A..GU */ + DEF -429 -599 -599 -599 + -479 -858 -1028 -1028 -1028 + -309 -688 -858 -858 -858 + -389 -768 -938 -938 -938 + -379 -758 -928 -928 -928 +/* AU.C..GU */ + DEF -259 -239 -239 -239 + -649 -858 -838 -838 -838 + -289 -498 -478 -478 -478 + -739 -948 -928 -928 -928 + -379 -588 -568 -568 -568 +/* AU.G..GU */ + DEF -339 -689 -689 -689 + -649 -938 -1288 -1288 -1288 + -289 -578 -928 -928 -928 + -739 -1028 -1378 -1378 -1378 + -379 -668 -1018 -1018 -1018 +/* AU.U..GU */ + DEF -329 -329 -329 -329 + -649 -928 -928 -928 -928 + -289 -568 -568 -568 -568 + -739 -1018 -1018 -1018 -1018 + -379 -658 -658 -658 -658 +/* AU.@..UG */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* AU.A..UG */ + DEF -429 -599 -599 -599 + -769 -1148 -1318 -1318 -1318 + -529 -908 -1078 -1078 -1078 + -709 -1088 -1258 -1258 -1258 + -599 -978 -1148 -1148 -1148 +/* AU.C..UG */ + DEF -259 -239 -239 -239 + -839 -1048 -1028 -1028 -1028 + -529 -738 -718 -718 -718 + -859 -1068 -1048 -1048 -1048 + -489 -698 -678 -678 -678 +/* AU.G..UG */ + DEF -339 -689 -689 -689 + -1009 -1298 -1648 -1648 -1648 + -409 -698 -1048 -1048 -1048 + -969 -1258 -1608 -1608 -1608 + -599 -888 -1238 -1238 -1238 +/* AU.U..UG */ + DEF -329 -329 -329 -329 + -859 -1138 -1138 -1138 -1138 + -529 -808 -808 -808 -808 + -859 -1138 -1138 -1138 -1138 + -409 -688 -688 -688 -688 +/* AU.@..AU */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* AU.A..AU */ + DEF -429 -599 -599 -599 + -479 -858 -1028 -1028 -1028 + -309 -688 -858 -858 -858 + -389 -768 -938 -938 -938 + -379 -758 -928 -928 -928 +/* AU.C..AU */ + DEF -259 -239 -239 -239 + -649 -858 -838 -838 -838 + -289 -498 -478 -478 -478 + -739 -948 -928 -928 -928 + -379 -588 -568 -568 -568 +/* AU.G..AU */ + DEF -339 -689 -689 -689 + -649 -938 -1288 -1288 -1288 + -289 -578 -928 -928 -928 + -739 -1028 -1378 -1378 -1378 + -379 -668 -1018 -1018 -1018 +/* AU.U..AU */ + DEF -329 -329 -329 -329 + -649 -928 -928 -928 -928 + -289 -568 -568 -568 -568 + -739 -1018 -1018 -1018 -1018 + -379 -658 -658 -658 -658 +/* AU.@..UA */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* AU.A..UA */ + DEF -429 -599 -599 -599 + -449 -828 -998 -998 -998 + -479 -858 -1028 -1028 -1028 + -429 -808 -978 -978 -978 + -329 -708 -878 -878 -878 +/* AU.C..UA */ + DEF -259 -239 -239 -239 + -679 -888 -868 -868 -868 + -559 -768 -748 -748 -748 + -729 -938 -918 -918 -918 + -189 -398 -378 -378 -378 +/* AU.G..UA */ + DEF -339 -689 -689 -689 + -939 -1228 -1578 -1578 -1578 + -249 -538 -888 -888 -888 + -939 -1228 -1578 -1578 -1578 + -329 -618 -968 -968 -968 +/* AU.U..UA */ + DEF -329 -329 -329 -329 + -639 -918 -918 -918 -918 + -229 -508 -508 -508 -508 + -729 -1008 -1008 -1008 -1008 + -190 -469 -469 -469 -469 +/* AU.@.. @ */ + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* AU.A.. @ */ + -100 -479 -649 -649 -649 + -100 -479 -649 -649 -649 + -100 -479 -649 -649 -649 + -100 -479 -649 -649 -649 + -100 -479 -649 -649 -649 +/* AU.C.. @ */ + -100 -309 -289 -289 -289 + -100 -309 -289 -289 -289 + -100 -309 -289 -289 -289 + -100 -309 -289 -289 -289 + -100 -309 -289 -289 -289 +/* AU.G.. @ */ + -100 -389 -739 -739 -739 + -100 -389 -739 -739 -739 + -100 -389 -739 -739 -739 + -100 -389 -739 -739 -739 + -100 -389 -739 -739 -739 +/* AU.U.. @ */ + -100 -379 -379 -379 -379 + -100 -379 -379 -379 -379 + -100 -379 -379 -379 -379 + -100 -379 -379 -379 -379 + -100 -379 -379 -379 -379 +/* UA.@..CG */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* UA.A..CG */ + DEF -399 -629 -889 -589 + -1079 -1428 -1658 -1918 -1618 + -569 -918 -1148 -1408 -1108 + -989 -1338 -1568 -1828 -1528 + -859 -1208 -1438 -1698 -1398 +/* UA.C..CG */ + DEF -429 -509 -199 -179 + -999 -1378 -1458 -1148 -1128 + -499 -878 -958 -648 -628 + -989 -1368 -1448 -1138 -1118 + -789 -1168 -1248 -938 -918 +/* UA.G..CG */ + DEF -379 -679 -889 -679 + -1079 -1408 -1708 -1918 -1708 + -569 -898 -1198 -1408 -1198 + -989 -1318 -1618 -1828 -1618 + -859 -1188 -1488 -1698 -1488 +/* UA.U..CG */ + DEF -279 -139 -279 -140 + -1079 -1308 -1168 -1308 -1169 + -719 -948 -808 -948 -809 + -989 -1218 -1078 -1218 -1079 + -909 -1138 -998 -1138 -999 +/* UA.@..GC */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* UA.A..GC */ + DEF -399 -629 -889 -589 + -569 -918 -1148 -1408 -1108 + -769 -1118 -1348 -1608 -1308 + -759 -1108 -1338 -1598 -1298 + -549 -898 -1128 -1388 -1088 +/* UA.C..GC */ + DEF -429 -509 -199 -179 + -929 -1308 -1388 -1078 -1058 + -359 -738 -818 -508 -488 + -789 -1168 -1248 -938 -918 + -549 -928 -1008 -698 -678 +/* UA.G..GC */ + DEF -379 -679 -889 -679 + -609 -938 -1238 -1448 -1238 + -359 -688 -988 -1198 -988 + -669 -998 -1298 -1508 -1298 + -549 -878 -1178 -1388 -1178 +/* UA.U..GC */ + DEF -279 -139 -279 -140 + -929 -1158 -1018 -1158 -1019 + -439 -668 -528 -668 -529 + -789 -1018 -878 -1018 -879 + -619 -848 -708 -848 -709 +/* UA.@..GU */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* UA.A..GU */ + DEF -399 -629 -889 -589 + -479 -828 -1058 -1318 -1018 + -309 -658 -888 -1148 -848 + -389 -738 -968 -1228 -928 + -379 -728 -958 -1218 -918 +/* UA.C..GU */ + DEF -429 -509 -199 -179 + -649 -1028 -1108 -798 -778 + -289 -668 -748 -438 -418 + -739 -1118 -1198 -888 -868 + -379 -758 -838 -528 -508 +/* UA.G..GU */ + DEF -379 -679 -889 -679 + -649 -978 -1278 -1488 -1278 + -289 -618 -918 -1128 -918 + -739 -1068 -1368 -1578 -1368 + -379 -708 -1008 -1218 -1008 +/* UA.U..GU */ + DEF -279 -139 -279 -140 + -649 -878 -738 -878 -739 + -289 -518 -378 -518 -379 + -739 -968 -828 -968 -829 + -379 -608 -468 -608 -469 +/* UA.@..UG */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* UA.A..UG */ + DEF -399 -629 -889 -589 + -769 -1118 -1348 -1608 -1308 + -529 -878 -1108 -1368 -1068 + -709 -1058 -1288 -1548 -1248 + -599 -948 -1178 -1438 -1138 +/* UA.C..UG */ + DEF -429 -509 -199 -179 + -839 -1218 -1298 -988 -968 + -529 -908 -988 -678 -658 + -859 -1238 -1318 -1008 -988 + -489 -868 -948 -638 -618 +/* UA.G..UG */ + DEF -379 -679 -889 -679 + -1009 -1338 -1638 -1848 -1638 + -409 -738 -1038 -1248 -1038 + -969 -1298 -1598 -1808 -1598 + -599 -928 -1228 -1438 -1228 +/* UA.U..UG */ + DEF -279 -139 -279 -140 + -859 -1088 -948 -1088 -949 + -529 -758 -618 -758 -619 + -859 -1088 -948 -1088 -949 + -409 -638 -498 -638 -499 +/* UA.@..AU */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* UA.A..AU */ + DEF -399 -629 -889 -589 + -479 -828 -1058 -1318 -1018 + -309 -658 -888 -1148 -848 + -389 -738 -968 -1228 -928 + -379 -728 -958 -1218 -918 +/* UA.C..AU */ + DEF -429 -509 -199 -179 + -649 -1028 -1108 -798 -778 + -289 -668 -748 -438 -418 + -739 -1118 -1198 -888 -868 + -379 -758 -838 -528 -508 +/* UA.G..AU */ + DEF -379 -679 -889 -679 + -649 -978 -1278 -1488 -1278 + -289 -618 -918 -1128 -918 + -739 -1068 -1368 -1578 -1368 + -379 -708 -1008 -1218 -1008 +/* UA.U..AU */ + DEF -279 -139 -279 -140 + -649 -878 -738 -878 -739 + -289 -518 -378 -518 -379 + -739 -968 -828 -968 -829 + -379 -608 -468 -608 -469 +/* UA.@..UA */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* UA.A..UA */ + DEF -399 -629 -889 -589 + -449 -798 -1028 -1288 -988 + -479 -828 -1058 -1318 -1018 + -429 -778 -1008 -1268 -968 + -329 -678 -908 -1168 -868 +/* UA.C..UA */ + DEF -429 -509 -199 -179 + -679 -1058 -1138 -828 -808 + -559 -938 -1018 -708 -688 + -729 -1108 -1188 -878 -858 + -189 -568 -648 -338 -318 +/* UA.G..UA */ + DEF -379 -679 -889 -679 + -939 -1268 -1568 -1778 -1568 + -249 -578 -878 -1088 -878 + -939 -1268 -1568 -1778 -1568 + -329 -658 -958 -1168 -958 +/* UA.U..UA */ + DEF -279 -139 -279 -140 + -639 -868 -728 -868 -729 + -229 -458 -318 -458 -319 + -729 -958 -818 -958 -819 + -190 -419 -279 -419 -280 +/* UA.@.. @ */ + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* UA.A.. @ */ + -100 -449 -679 -939 -639 + -100 -449 -679 -939 -639 + -100 -449 -679 -939 -639 + -100 -449 -679 -939 -639 + -100 -449 -679 -939 -639 +/* UA.C.. @ */ + -100 -479 -559 -249 -229 + -100 -479 -559 -249 -229 + -100 -479 -559 -249 -229 + -100 -479 -559 -249 -229 + -100 -479 -559 -249 -229 +/* UA.G.. @ */ + -100 -429 -729 -939 -729 + -100 -429 -729 -939 -729 + -100 -429 -729 -939 -729 + -100 -429 -729 -939 -729 + -100 -429 -729 -939 -729 +/* UA.U.. @ */ + -100 -329 -189 -329 -190 + -100 -329 -189 -329 -190 + -100 -329 -189 -329 -190 + -100 -329 -189 -329 -190 + -100 -329 -189 -329 -190 +/* @.@..CG */ + DEF DEF DEF DEF DEF + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.A..CG */ + DEF DEF DEF DEF DEF + -1079 -1079 -1079 -1079 -1079 + -569 -569 -569 -569 -569 + -989 -989 -989 -989 -989 + -859 -859 -859 -859 -859 +/* @.C..CG */ + DEF DEF DEF DEF DEF + -999 -999 -999 -999 -999 + -499 -499 -499 -499 -499 + -989 -989 -989 -989 -989 + -789 -789 -789 -789 -789 +/* @.G..CG */ + DEF DEF DEF DEF DEF + -1079 -1079 -1079 -1079 -1079 + -569 -569 -569 -569 -569 + -989 -989 -989 -989 -989 + -859 -859 -859 -859 -859 +/* @.U..CG */ + DEF DEF DEF DEF DEF + -1079 -1079 -1079 -1079 -1079 + -719 -719 -719 -719 -719 + -989 -989 -989 -989 -989 + -909 -909 -909 -909 -909 +/* @.@..GC */ + DEF DEF DEF DEF DEF + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.A..GC */ + DEF DEF DEF DEF DEF + -569 -569 -569 -569 -569 + -769 -769 -769 -769 -769 + -759 -759 -759 -759 -759 + -549 -549 -549 -549 -549 +/* @.C..GC */ + DEF DEF DEF DEF DEF + -929 -929 -929 -929 -929 + -359 -359 -359 -359 -359 + -789 -789 -789 -789 -789 + -549 -549 -549 -549 -549 +/* @.G..GC */ + DEF DEF DEF DEF DEF + -609 -609 -609 -609 -609 + -359 -359 -359 -359 -359 + -669 -669 -669 -669 -669 + -549 -549 -549 -549 -549 +/* @.U..GC */ + DEF DEF DEF DEF DEF + -929 -929 -929 -929 -929 + -439 -439 -439 -439 -439 + -789 -789 -789 -789 -789 + -619 -619 -619 -619 -619 +/* @.@..GU */ + DEF DEF DEF DEF DEF + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.A..GU */ + DEF DEF DEF DEF DEF + -479 -479 -479 -479 -479 + -309 -309 -309 -309 -309 + -389 -389 -389 -389 -389 + -379 -379 -379 -379 -379 +/* @.C..GU */ + DEF DEF DEF DEF DEF + -649 -649 -649 -649 -649 + -289 -289 -289 -289 -289 + -739 -739 -739 -739 -739 + -379 -379 -379 -379 -379 +/* @.G..GU */ + DEF DEF DEF DEF DEF + -649 -649 -649 -649 -649 + -289 -289 -289 -289 -289 + -739 -739 -739 -739 -739 + -379 -379 -379 -379 -379 +/* @.U..GU */ + DEF DEF DEF DEF DEF + -649 -649 -649 -649 -649 + -289 -289 -289 -289 -289 + -739 -739 -739 -739 -739 + -379 -379 -379 -379 -379 +/* @.@..UG */ + DEF DEF DEF DEF DEF + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.A..UG */ + DEF DEF DEF DEF DEF + -769 -769 -769 -769 -769 + -529 -529 -529 -529 -529 + -709 -709 -709 -709 -709 + -599 -599 -599 -599 -599 +/* @.C..UG */ + DEF DEF DEF DEF DEF + -839 -839 -839 -839 -839 + -529 -529 -529 -529 -529 + -859 -859 -859 -859 -859 + -489 -489 -489 -489 -489 +/* @.G..UG */ + DEF DEF DEF DEF DEF + -1009 -1009 -1009 -1009 -1009 + -409 -409 -409 -409 -409 + -969 -969 -969 -969 -969 + -599 -599 -599 -599 -599 +/* @.U..UG */ + DEF DEF DEF DEF DEF + -859 -859 -859 -859 -859 + -529 -529 -529 -529 -529 + -859 -859 -859 -859 -859 + -409 -409 -409 -409 -409 +/* @.@..AU */ + DEF DEF DEF DEF DEF + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.A..AU */ + DEF DEF DEF DEF DEF + -479 -479 -479 -479 -479 + -309 -309 -309 -309 -309 + -389 -389 -389 -389 -389 + -379 -379 -379 -379 -379 +/* @.C..AU */ + DEF DEF DEF DEF DEF + -649 -649 -649 -649 -649 + -289 -289 -289 -289 -289 + -739 -739 -739 -739 -739 + -379 -379 -379 -379 -379 +/* @.G..AU */ + DEF DEF DEF DEF DEF + -649 -649 -649 -649 -649 + -289 -289 -289 -289 -289 + -739 -739 -739 -739 -739 + -379 -379 -379 -379 -379 +/* @.U..AU */ + DEF DEF DEF DEF DEF + -649 -649 -649 -649 -649 + -289 -289 -289 -289 -289 + -739 -739 -739 -739 -739 + -379 -379 -379 -379 -379 +/* @.@..UA */ + DEF DEF DEF DEF DEF + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.A..UA */ + DEF DEF DEF DEF DEF + -449 -449 -449 -449 -449 + -479 -479 -479 -479 -479 + -429 -429 -429 -429 -429 + -329 -329 -329 -329 -329 +/* @.C..UA */ + DEF DEF DEF DEF DEF + -679 -679 -679 -679 -679 + -559 -559 -559 -559 -559 + -729 -729 -729 -729 -729 + -189 -189 -189 -189 -189 +/* @.G..UA */ + DEF DEF DEF DEF DEF + -939 -939 -939 -939 -939 + -249 -249 -249 -249 -249 + -939 -939 -939 -939 -939 + -329 -329 -329 -329 -329 +/* @.U..UA */ + DEF DEF DEF DEF DEF + -639 -639 -639 -639 -639 + -229 -229 -229 -229 -229 + -729 -729 -729 -729 -729 + -190 -190 -190 -190 -190 +/* @.@.. @ */ + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.A.. @ */ + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.C.. @ */ + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.G.. @ */ + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.U.. @ */ + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + +# int22 +/* CG.AA..CG */ + 151 193 82 200 + 204 217 113 200 + 68 88 -23 200 + 200 200 200 200 +/* CG.AC..CG */ + 193 176 102 200 + 202 222 177 200 + 200 200 200 200 + 156 176 131 200 +/* CG.AG..CG */ + 82 102 -33 200 + 200 200 200 200 + 116 136 25 200 + -15 -61 -46 200 +/* CG.AU..CG */ + 200 200 200 200 + 171 191 146 200 + 117 71 86 200 + 194 148 163 200 +/* CG.CA..CG */ + 204 202 200 171 + 199 233 200 202 + 99 163 200 132 + 200 200 200 200 +/* CG.CC..CG */ + 217 222 200 191 + 233 209 200 200 + 200 200 200 200 + 187 185 200 154 +/* CG.CG..CG */ + 113 177 200 146 + 200 200 200 200 + 147 145 200 114 + DEF 14 200 -17 +/* CG.CU..CG */ + 200 200 200 200 + 202 200 200 146 + 82 146 200 115 + 159 157 200 126 +/* CG.GA..CG */ + 68 200 116 117 + 99 200 147 82 + -61 200 11 72 + 200 200 200 200 +/* CG.GC..CG */ + 88 200 136 71 + 163 200 145 146 + 200 200 200 200 + 117 200 99 100 +/* CG.GG..CG */ + -23 200 25 86 + 200 200 200 200 + 11 200 37 60 + -60 200 -72 -203 +/* CG.GU..CG */ + 200 200 200 200 + 132 200 114 115 + 72 200 60 -95 + 149 200 137 132 +/* CG.UA..CG */ + 200 156 -15 194 + 200 187 DEF 159 + 200 117 -60 149 + 200 200 200 200 +/* CG.UC..CG */ + 200 176 -61 148 + 200 185 14 157 + 200 200 200 200 + 200 117 -32 111 +/* CG.UG..CG */ + 200 131 -46 163 + 200 200 200 200 + 200 99 -72 137 + 200 -32 -358 0 +/* CG.UU..CG */ + 200 200 200 200 + 200 154 -17 126 + 200 100 -203 132 + 200 111 0 60 +/* CG.AA..GC */ + 130 150 39 200 + 113 126 22 200 + 11 31 -80 200 + 200 200 200 200 +/* CG.AC..GC */ + 108 121 17 200 + 98 118 73 200 + 200 200 200 200 + 85 105 60 200 +/* CG.AG..GC */ + 48 68 -43 200 + 200 200 200 200 + 88 108 -3 200 + -36 -82 -67 200 +/* CG.AU..GC */ + 200 200 200 200 + 147 167 122 200 + -5 -51 -36 200 + 89 43 58 200 +/* CG.CA..GC */ + 161 159 200 128 + 137 142 200 111 + 42 106 200 75 + 200 200 200 200 +/* CG.CC..GC */ + 132 137 200 106 + 129 127 200 96 + 200 200 200 200 + 116 114 200 83 +/* CG.CG..GC */ + 79 143 200 112 + 200 200 200 200 + 119 117 200 86 + -71 -7 200 -38 +/* CG.CU..GC */ + 200 200 200 200 + 178 176 200 145 + -40 24 200 -7 + 54 52 200 21 +/* CG.GA..GC */ + 25 200 73 74 + 8 200 56 -9 + -94 200 -46 15 + 200 200 200 200 +/* CG.GC..GC */ + 3 200 51 -14 + 59 200 41 42 + 200 200 200 200 + 46 200 28 29 +/* CG.GG..GC */ + -57 200 -9 52 + 200 200 200 200 + -17 200 31 32 + -81 200 -93 -224 +/* CG.GU..GC */ + 200 200 200 200 + 108 200 90 91 + DEF 200 -62 -193 + 44 200 32 27 +/* CG.UA..GC */ + 200 113 -58 151 + 200 96 -141 68 + 200 60 -117 92 + 200 200 200 200 +/* CG.UC..GC */ + 200 91 -146 63 + 200 81 -90 53 + 200 200 200 200 + 200 68 -103 40 +/* CG.UG..GC */ + 200 97 -80 129 + 200 200 200 200 + 200 71 -100 109 + 200 -53 -356 -21 +/* CG.UU..GC */ + 200 200 200 200 + 200 130 -41 102 + 200 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GC.GU..UG */ + -1518 -1548 -1428 -1548 + -1188 -1218 -1098 -1218 + -1518 -1548 -1428 -1548 + -1068 -1098 -978 -1098 +/* GC.UA..UG */ + -1218 -1218 -1218 -1288 + -978 -978 -978 -1048 + -1158 -1158 -1158 -1228 + -1048 -1048 -1048 -1118 +/* GC.UC..UG */ + -1288 -1288 -1288 -1358 + -978 -978 -978 -1048 + -1308 -1308 -1308 -1378 + -938 -938 -938 -1008 +/* GC.UG..UG */ + -1458 -1458 -1458 -1528 + -858 -858 -858 -928 + -1418 -1418 -1418 -1488 + -1048 -1048 -1048 -1118 +/* GC.UU..UG */ + -1308 -1308 -1308 -1378 + -978 -978 -978 -1048 + -1308 -1308 -1308 -1378 + -858 -858 -858 -928 +/* GC.AA..AU */ + -948 -1308 -988 -1308 + -778 -1138 -818 -1138 + -858 -1218 -898 -1218 + -848 -1208 -888 -1208 +/* GC.AC..AU */ + -1118 -1478 -1158 -1478 + -758 -1118 -798 -1118 + -1208 -1568 -1248 -1568 + -848 -1208 -888 -1208 +/* GC.AG..AU */ + -1118 -1478 -1158 -1478 + -758 -1118 -798 -1118 + -1208 -1568 -1248 -1568 + -848 -1208 -888 -1208 +/* GC.AU..AU */ + -1118 -1478 -1158 -1478 + -758 -1118 -798 -1118 + 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*/ + -1388 -1388 -1388 -1458 + -698 -698 -698 -768 + -1388 -1388 -1388 -1458 + -778 -778 -778 -848 +/* GC.UU..UA */ + -1088 -1088 -1088 -1158 + -678 -678 -678 -748 + -1178 -1178 -1178 -1248 + -639 -639 -639 -709 +/* GU.AA..CG */ + -1458 -1628 -1628 -1628 + -948 -1118 -1118 -1118 + -1368 -1538 -1538 -1538 + -1238 -1408 -1408 -1408 +/* GU.AC..CG */ + -1378 -1548 -1548 -1548 + -878 -1048 -1048 -1048 + -1368 -1538 -1538 -1538 + -1168 -1338 -1338 -1338 +/* GU.AG..CG */ + -1458 -1628 -1628 -1628 + -948 -1118 -1118 -1118 + -1368 -1538 -1538 -1538 + -1238 -1408 -1408 -1408 +/* GU.AU..CG */ + -1458 -1628 -1628 -1628 + -1098 -1268 -1268 -1268 + -1368 -1538 -1538 -1538 + -1288 -1458 -1458 -1458 +/* GU.CA..CG */ + -1288 -1268 -1268 -1268 + -778 -758 -758 -758 + -1198 -1178 -1178 -1178 + -1068 -1048 -1048 -1048 +/* GU.CC..CG */ + -1208 -1188 -1188 -1188 + -708 -688 -688 -688 + -1198 -1178 -1178 -1178 + -998 -978 -978 -978 +/* GU.CG..CG */ + -1288 -1268 -1268 -1268 + -778 -758 -758 -758 + -1198 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GU.UU..CG */ + -1358 -1358 -1358 -1358 + -998 -998 -998 -998 + -1268 -1268 -1268 -1268 + -1188 -1188 -1188 -1188 +/* GU.AA..GC */ + -948 -1118 -1118 -1118 + -1148 -1318 -1318 -1318 + -1138 -1308 -1308 -1308 + -928 -1098 -1098 -1098 +/* GU.AC..GC */ + -1308 -1478 -1478 -1478 + -738 -908 -908 -908 + -1168 -1338 -1338 -1338 + -928 -1098 -1098 -1098 +/* GU.AG..GC */ + -988 -1158 -1158 -1158 + -738 -908 -908 -908 + -1048 -1218 -1218 -1218 + -928 -1098 -1098 -1098 +/* GU.AU..GC */ + -1308 -1478 -1478 -1478 + -818 -988 -988 -988 + -1168 -1338 -1338 -1338 + -998 -1168 -1168 -1168 +/* GU.CA..GC */ + -778 -758 -758 -758 + -978 -958 -958 -958 + -968 -948 -948 -948 + -758 -738 -738 -738 +/* GU.CC..GC */ + -1138 -1118 -1118 -1118 + -568 -548 -548 -548 + -998 -978 -978 -978 + -758 -738 -738 -738 +/* GU.CG..GC */ + -818 -798 -798 -798 + -568 -548 -548 -548 + -878 -858 -858 -858 + -758 -738 -738 -738 +/* GU.CU..GC */ + -1138 -1118 -1118 -1118 + -648 -628 -628 -628 + -998 -978 -978 -978 + -828 -808 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AU.CA..AU */ + -688 -668 -668 -668 + -518 -498 -498 -498 + -598 -578 -578 -578 + -588 -568 -568 -568 +/* AU.CC..AU */ + -858 -838 -838 -838 + -498 -478 -478 -478 + -948 -928 -928 -928 + -588 -568 -568 -568 +/* AU.CG..AU */ + -858 -838 -838 -838 + -498 -478 -478 -478 + -948 -928 -928 -928 + -588 -568 -568 -568 +/* AU.CU..AU */ + -858 -838 -838 -838 + -498 -478 -478 -478 + -948 -928 -928 -928 + -588 -568 -568 -568 +/* AU.GA..AU */ + -768 -1118 -1118 -1118 + -598 -948 -948 -948 + -678 -1028 -1028 -1028 + -668 -1018 -1018 -1018 +/* AU.GC..AU */ + -938 -1288 -1288 -1288 + -578 -928 -928 -928 + -1028 -1378 -1378 -1378 + -668 -1018 -1018 -1018 +/* AU.GG..AU */ + -938 -1288 -1288 -1288 + -578 -928 -928 -928 + -1028 -1378 -1378 -1378 + -668 -1018 -1018 -1018 +/* AU.GU..AU */ + -938 -1288 -1288 -1288 + -578 -928 -928 -928 + -1028 -1378 -1378 -1378 + -668 -1018 -1018 -1018 +/* AU.UA..AU */ + -758 -758 -758 -758 + -588 -588 -588 -588 + -668 -668 -668 -668 + -658 -658 -658 -658 +/* AU.UC..AU */ + -928 -928 -928 -928 + -568 -568 -568 -568 + -1018 -1018 -1018 -1018 + -658 -658 -658 -658 +/* AU.UG..AU */ + -928 -928 -928 -928 + -568 -568 -568 -568 + -1018 -1018 -1018 -1018 + -658 -658 -658 -658 +/* AU.UU..AU */ + -928 -928 -928 -928 + -568 -568 -568 -568 + -1018 -1018 -1018 -1018 + -658 -658 -658 -658 +/* AU.AA..UA */ + -828 -998 -998 -998 + -858 -1028 -1028 -1028 + -808 -978 -978 -978 + -708 -878 -878 -878 +/* AU.AC..UA */ + -1058 -1228 -1228 -1228 + -938 -1108 -1108 -1108 + -1108 -1278 -1278 -1278 + -568 -738 -738 -738 +/* AU.AG..UA */ + -1318 -1488 -1488 -1488 + -628 -798 -798 -798 + -1318 -1488 -1488 -1488 + -708 -878 -878 -878 +/* AU.AU..UA */ + -1018 -1188 -1188 -1188 + -608 -778 -778 -778 + -1108 -1278 -1278 -1278 + -569 -739 -739 -739 +/* AU.CA..UA */ + -658 -638 -638 -638 + -688 -668 -668 -668 + -638 -618 -618 -618 + -538 -518 -518 -518 +/* AU.CC..UA */ + -888 -868 -868 -868 + -768 -748 -748 -748 + -938 -918 -918 -918 + -398 -378 -378 -378 +/* AU.CG..UA */ + -1148 -1128 -1128 -1128 + -458 -438 -438 -438 + -1148 -1128 -1128 -1128 + -538 -518 -518 -518 +/* AU.CU..UA */ + -848 -828 -828 -828 + -438 -418 -418 -418 + -938 -918 -918 -918 + -399 -379 -379 -379 +/* AU.GA..UA */ + -738 -1088 -1088 -1088 + -768 -1118 -1118 -1118 + -718 -1068 -1068 -1068 + -618 -968 -968 -968 +/* AU.GC..UA */ + -968 -1318 -1318 -1318 + -848 -1198 -1198 -1198 + -1018 -1368 -1368 -1368 + -478 -828 -828 -828 +/* AU.GG..UA */ + -1228 -1578 -1578 -1578 + -538 -888 -888 -888 + -1228 -1578 -1578 -1578 + -618 -968 -968 -968 +/* AU.GU..UA */ + -928 -1278 -1278 -1278 + -518 -868 -868 -868 + -1018 -1368 -1368 -1368 + -479 -829 -829 -829 +/* AU.UA..UA */ + -728 -728 -728 -728 + -758 -758 -758 -758 + -708 -708 -708 -708 + -608 -608 -608 -608 +/* AU.UC..UA */ + -958 -958 -958 -958 + -838 -838 -838 -838 + -1008 -1008 -1008 -1008 + -468 -468 -468 -468 +/* AU.UG..UA */ + -1218 -1218 -1218 -1218 + -528 -528 -528 -528 + -1218 -1218 -1218 -1218 + -608 -608 -608 -608 +/* AU.UU..UA */ + -918 -918 -918 -918 + -508 -508 -508 -508 + -1008 -1008 -1008 -1008 + -469 -469 -469 -469 +/* UA.AA..CG */ + -1428 -1658 -1918 -1618 + -918 -1148 -1408 -1108 + -1338 -1568 -1828 -1528 + -1208 -1438 -1698 -1398 +/* UA.AC..CG */ + -1348 -1578 -1838 -1538 + -848 -1078 -1338 -1038 + -1338 -1568 -1828 -1528 + -1138 -1368 -1628 -1328 +/* UA.AG..CG */ + -1428 -1658 -1918 -1618 + -918 -1148 -1408 -1108 + -1338 -1568 -1828 -1528 + -1208 -1438 -1698 -1398 +/* UA.AU..CG */ + -1428 -1658 -1918 -1618 + -1068 -1298 -1558 -1258 + -1338 -1568 -1828 -1528 + -1258 -1488 -1748 -1448 +/* UA.CA..CG */ + -1458 -1538 -1228 -1208 + -948 -1028 -718 -698 + -1368 -1448 -1138 -1118 + -1238 -1318 -1008 -988 +/* UA.CC..CG */ + -1378 -1458 -1148 -1128 + -878 -958 -648 -628 + -1368 -1448 -1138 -1118 + -1168 -1248 -938 -918 +/* UA.CG..CG */ + -1458 -1538 -1228 -1208 + -948 -1028 -718 -698 + -1368 -1448 -1138 -1118 + -1238 -1318 -1008 -988 +/* UA.CU..CG */ + -1458 -1538 -1228 -1208 + -1098 -1178 -868 -848 + -1368 -1448 -1138 -1118 + -1288 -1368 -1058 -1038 +/* UA.GA..CG */ + -1408 -1708 -1918 -1708 + -898 -1198 -1408 -1198 + -1318 -1618 -1828 -1618 + -1188 -1488 -1698 -1488 +/* UA.GC..CG */ + -1328 -1628 -1838 -1628 + -828 -1128 -1338 -1128 + -1318 -1618 -1828 -1618 + -1118 -1418 -1628 -1418 +/* UA.GG..CG */ + -1408 -1708 -1918 -1708 + -898 -1198 -1408 -1198 + -1318 -1618 -1828 -1618 + -1188 -1488 -1698 -1488 +/* UA.GU..CG */ + -1408 -1708 -1918 -1708 + -1048 -1348 -1558 -1348 + -1318 -1618 -1828 -1618 + -1238 -1538 -1748 -1538 +/* UA.UA..CG */ + -1308 -1168 -1308 -1169 + -798 -658 -798 -659 + -1218 -1078 -1218 -1079 + -1088 -948 -1088 -949 +/* UA.UC..CG */ + -1228 -1088 -1228 -1089 + -728 -588 -728 -589 + -1218 -1078 -1218 -1079 + -1018 -878 -1018 -879 +/* UA.UG..CG */ + -1308 -1168 -1308 -1169 + -798 -658 -798 -659 + -1218 -1078 -1218 -1079 + -1088 -948 -1088 -949 +/* UA.UU..CG */ + -1308 -1168 -1308 -1169 + -948 -808 -948 -809 + -1218 -1078 -1218 -1079 + -1138 -998 -1138 -999 +/* UA.AA..GC */ + -918 -1148 -1408 -1108 + -1118 -1348 -1608 -1308 + -1108 -1338 -1598 -1298 + -898 -1128 -1388 -1088 +/* UA.AC..GC */ + -1278 -1508 -1768 -1468 + -708 -938 -1198 -898 + -1138 -1368 -1628 -1328 + -898 -1128 -1388 -1088 +/* UA.AG..GC */ + -958 -1188 -1448 -1148 + -708 -938 -1198 -898 + -1018 -1248 -1508 -1208 + -898 -1128 -1388 -1088 +/* UA.AU..GC */ + -1278 -1508 -1768 -1468 + -788 -1018 -1278 -978 + -1138 -1368 -1628 -1328 + -968 -1198 -1458 -1158 +/* UA.CA..GC */ + -948 -1028 -718 -698 + -1148 -1228 -918 -898 + -1138 -1218 -908 -888 + -928 -1008 -698 -678 +/* UA.CC..GC */ + -1308 -1388 -1078 -1058 + -738 -818 -508 -488 + -1168 -1248 -938 -918 + -928 -1008 -698 -678 +/* UA.CG..GC */ + -988 -1068 -758 -738 + -738 -818 -508 -488 + -1048 -1128 -818 -798 + -928 -1008 -698 -678 +/* UA.CU..GC */ + -1308 -1388 -1078 -1058 + -818 -898 -588 -568 + -1168 -1248 -938 -918 + -998 -1078 -768 -748 +/* UA.GA..GC */ + -898 -1198 -1408 -1198 + -1098 -1398 -1608 -1398 + -1088 -1388 -1598 -1388 + -878 -1178 -1388 -1178 +/* UA.GC..GC */ + -1258 -1558 -1768 -1558 + -688 -988 -1198 -988 + -1118 -1418 -1628 -1418 + -878 -1178 -1388 -1178 +/* UA.GG..GC */ + -938 -1238 -1448 -1238 + -688 -988 -1198 -988 + -998 -1298 -1508 -1298 + -878 -1178 -1388 -1178 +/* UA.GU..GC */ + -1258 -1558 -1768 -1558 + -768 -1068 -1278 -1068 + -1118 -1418 -1628 -1418 + -948 -1248 -1458 -1248 +/* UA.UA..GC */ + -798 -658 -798 -659 + -998 -858 -998 -859 + -988 -848 -988 -849 + -778 -638 -778 -639 +/* UA.UC..GC */ + -1158 -1018 -1158 -1019 + -588 -448 -588 -449 + -1018 -878 -1018 -879 + -778 -638 -778 -639 +/* UA.UG..GC */ + -838 -698 -838 -699 + -588 -448 -588 -449 + -898 -758 -898 -759 + -778 -638 -778 -639 +/* UA.UU..GC */ + -1158 -1018 -1158 -1019 + -668 -528 -668 -529 + -1018 -878 -1018 -879 + -848 -708 -848 -709 +/* UA.AA..GU */ + -828 -1058 -1318 -1018 + -658 -888 -1148 -848 + -738 -968 -1228 -928 + -728 -958 -1218 -918 +/* UA.AC..GU */ + -998 -1228 -1488 -1188 + -638 -868 -1128 -828 + -1088 -1318 -1578 -1278 + -728 -958 -1218 -918 +/* UA.AG..GU */ + -998 -1228 -1488 -1188 + -638 -868 -1128 -828 + -1088 -1318 -1578 -1278 + -728 -958 -1218 -918 +/* UA.AU..GU */ + -998 -1228 -1488 -1188 + -638 -868 -1128 -828 + -1088 -1318 -1578 -1278 + -728 -958 -1218 -918 +/* UA.CA..GU */ + -858 -938 -628 -608 + -688 -768 -458 -438 + -768 -848 -538 -518 + -758 -838 -528 -508 +/* UA.CC..GU */ + -1028 -1108 -798 -778 + -668 -748 -438 -418 + -1118 -1198 -888 -868 + -758 -838 -528 -508 +/* UA.CG..GU */ + -1028 -1108 -798 -778 + -668 -748 -438 -418 + -1118 -1198 -888 -868 + -758 -838 -528 -508 +/* UA.CU..GU */ + -1028 -1108 -798 -778 + -668 -748 -438 -418 + -1118 -1198 -888 -868 + -758 -838 -528 -508 +/* UA.GA..GU */ + -808 -1108 -1318 -1108 + -638 -938 -1148 -938 + -718 -1018 -1228 -1018 + -708 -1008 -1218 -1008 +/* UA.GC..GU */ + -978 -1278 -1488 -1278 + -618 -918 -1128 -918 + -1068 -1368 -1578 -1368 + -708 -1008 -1218 -1008 +/* UA.GG..GU */ + -978 -1278 -1488 -1278 + -618 -918 -1128 -918 + -1068 -1368 -1578 -1368 + -708 -1008 -1218 -1008 +/* UA.GU..GU */ + -978 -1278 -1488 -1278 + -618 -918 -1128 -918 + -1068 -1368 -1578 -1368 + -708 -1008 -1218 -1008 +/* UA.UA..GU */ + -708 -568 -708 -569 + -538 -398 -538 -399 + -618 -478 -618 -479 + -608 -468 -608 -469 +/* UA.UC..GU */ + -878 -738 -878 -739 + -518 -378 -518 -379 + -968 -828 -968 -829 + -608 -468 -608 -469 +/* UA.UG..GU */ + -878 -738 -878 -739 + -518 -378 -518 -379 + -968 -828 -968 -829 + -608 -468 -608 -469 +/* UA.UU..GU */ + -878 -738 -878 -739 + -518 -378 -518 -379 + -968 -828 -968 -829 + -608 -468 -608 -469 +/* UA.AA..UG */ + -1118 -1348 -1608 -1308 + -878 -1108 -1368 -1068 + -1058 -1288 -1548 -1248 + -948 -1178 -1438 -1138 +/* UA.AC..UG */ + -1188 -1418 -1678 -1378 + -878 -1108 -1368 -1068 + -1208 -1438 -1698 -1398 + -838 -1068 -1328 -1028 +/* UA.AG..UG */ + -1358 -1588 -1848 -1548 + -758 -988 -1248 -948 + -1318 -1548 -1808 -1508 + -948 -1178 -1438 -1138 +/* UA.AU..UG */ + -1208 -1438 -1698 -1398 + -878 -1108 -1368 -1068 + -1208 -1438 -1698 -1398 + -758 -988 -1248 -948 +/* UA.CA..UG */ + -1148 -1228 -918 -898 + -908 -988 -678 -658 + -1088 -1168 -858 -838 + -978 -1058 -748 -728 +/* UA.CC..UG */ + -1218 -1298 -988 -968 + -908 -988 -678 -658 + -1238 -1318 -1008 -988 + -868 -948 -638 -618 +/* UA.CG..UG */ + -1388 -1468 -1158 -1138 + -788 -868 -558 -538 + -1348 -1428 -1118 -1098 + -978 -1058 -748 -728 +/* UA.CU..UG */ + -1238 -1318 -1008 -988 + -908 -988 -678 -658 + -1238 -1318 -1008 -988 + -788 -868 -558 -538 +/* UA.GA..UG */ + -1098 -1398 -1608 -1398 + -858 -1158 -1368 -1158 + -1038 -1338 -1548 -1338 + -928 -1228 -1438 -1228 +/* UA.GC..UG */ + -1168 -1468 -1678 -1468 + -858 -1158 -1368 -1158 + -1188 -1488 -1698 -1488 + -818 -1118 -1328 -1118 +/* UA.GG..UG */ + -1338 -1638 -1848 -1638 + -738 -1038 -1248 -1038 + -1298 -1598 -1808 -1598 + -928 -1228 -1438 -1228 +/* UA.GU..UG */ + -1188 -1488 -1698 -1488 + -858 -1158 -1368 -1158 + -1188 -1488 -1698 -1488 + -738 -1038 -1248 -1038 +/* UA.UA..UG */ + -998 -858 -998 -859 + -758 -618 -758 -619 + -938 -798 -938 -799 + -828 -688 -828 -689 +/* UA.UC..UG */ + -1068 -928 -1068 -929 + -758 -618 -758 -619 + -1088 -948 -1088 -949 + -718 -578 -718 -579 +/* UA.UG..UG */ + -1238 -1098 -1238 -1099 + -638 -498 -638 -499 + -1198 -1058 -1198 -1059 + -828 -688 -828 -689 +/* UA.UU..UG */ + -1088 -948 -1088 -949 + -758 -618 -758 -619 + -1088 -948 -1088 -949 + -638 -498 -638 -499 +/* UA.AA..AU */ + -828 -1058 -1318 -1018 + -658 -888 -1148 -848 + -738 -968 -1228 -928 + -728 -958 -1218 -918 +/* UA.AC..AU */ + -998 -1228 -1488 -1188 + -638 -868 -1128 -828 + -1088 -1318 -1578 -1278 + -728 -958 -1218 -918 +/* UA.AG..AU */ + -998 -1228 -1488 -1188 + -638 -868 -1128 -828 + -1088 -1318 -1578 -1278 + -728 -958 -1218 -918 +/* UA.AU..AU */ + -998 -1228 -1488 -1188 + -638 -868 -1128 -828 + -1088 -1318 -1578 -1278 + -728 -958 -1218 -918 +/* UA.CA..AU */ + -858 -938 -628 -608 + -688 -768 -458 -438 + -768 -848 -538 -518 + -758 -838 -528 -508 +/* UA.CC..AU */ + -1028 -1108 -798 -778 + -668 -748 -438 -418 + -1118 -1198 -888 -868 + -758 -838 -528 -508 +/* UA.CG..AU */ + -1028 -1108 -798 -778 + -668 -748 -438 -418 + -1118 -1198 -888 -868 + -758 -838 -528 -508 +/* UA.CU..AU */ + -1028 -1108 -798 -778 + -668 -748 -438 -418 + -1118 -1198 -888 -868 + -758 -838 -528 -508 +/* UA.GA..AU */ + -808 -1108 -1318 -1108 + -638 -938 -1148 -938 + -718 -1018 -1228 -1018 + -708 -1008 -1218 -1008 +/* UA.GC..AU */ + -978 -1278 -1488 -1278 + -618 -918 -1128 -918 + -1068 -1368 -1578 -1368 + -708 -1008 -1218 -1008 +/* UA.GG..AU */ + -978 -1278 -1488 -1278 + -618 -918 -1128 -918 + -1068 -1368 -1578 -1368 + -708 -1008 -1218 -1008 +/* UA.GU..AU */ + -978 -1278 -1488 -1278 + -618 -918 -1128 -918 + -1068 -1368 -1578 -1368 + -708 -1008 -1218 -1008 +/* UA.UA..AU */ + -708 -568 -708 -569 + -538 -398 -538 -399 + -618 -478 -618 -479 + -608 -468 -608 -469 +/* UA.UC..AU */ + -878 -738 -878 -739 + -518 -378 -518 -379 + -968 -828 -968 -829 + -608 -468 -608 -469 +/* UA.UG..AU */ + -878 -738 -878 -739 + -518 -378 -518 -379 + -968 -828 -968 -829 + -608 -468 -608 -469 +/* UA.UU..AU */ + -878 -738 -878 -739 + -518 -378 -518 -379 + -968 -828 -968 -829 + -608 -468 -608 -469 +/* UA.AA..UA */ + -798 -1028 -1288 -988 + -828 -1058 -1318 -1018 + -778 -1008 -1268 -968 + -678 -908 -1168 -868 +/* UA.AC..UA */ + -1028 -1258 -1518 -1218 + -908 -1138 -1398 -1098 + -1078 -1308 -1568 -1268 + -538 -768 -1028 -728 +/* UA.AG..UA */ + -1288 -1518 -1778 -1478 + -598 -828 -1088 -788 + -1288 -1518 -1778 -1478 + -678 -908 -1168 -868 +/* UA.AU..UA */ + -988 -1218 -1478 -1178 + -578 -808 -1068 -768 + -1078 -1308 -1568 -1268 + -539 -769 -1029 -729 +/* UA.CA..UA */ + -828 -908 -598 -578 + -858 -938 -628 -608 + -808 -888 -578 -558 + -708 -788 -478 -458 +/* UA.CC..UA */ + -1058 -1138 -828 -808 + -938 -1018 -708 -688 + -1108 -1188 -878 -858 + -568 -648 -338 -318 +/* UA.CG..UA */ + -1318 -1398 -1088 -1068 + -628 -708 -398 -378 + -1318 -1398 -1088 -1068 + -708 -788 -478 -458 +/* UA.CU..UA */ + -1018 -1098 -788 -768 + -608 -688 -378 -358 + -1108 -1188 -878 -858 + -569 -649 -339 -319 +/* UA.GA..UA */ + -778 -1078 -1288 -1078 + -808 -1108 -1318 -1108 + -758 -1058 -1268 -1058 + -658 -958 -1168 -958 +/* UA.GC..UA */ + -1008 -1308 -1518 -1308 + -888 -1188 -1398 -1188 + -1058 -1358 -1568 -1358 + -518 -818 -1028 -818 +/* UA.GG..UA */ + -1268 -1568 -1778 -1568 + -578 -878 -1088 -878 + -1268 -1568 -1778 -1568 + -658 -958 -1168 -958 +/* UA.GU..UA */ + -968 -1268 -1478 -1268 + -558 -858 -1068 -858 + -1058 -1358 -1568 -1358 + -519 -819 -1029 -819 +/* UA.UA..UA */ + -678 -538 -678 -539 + -708 -568 -708 -569 + -658 -518 -658 -519 + -558 -418 -558 -419 +/* UA.UC..UA */ + -908 -768 -908 -769 + -788 -648 -788 -649 + -958 -818 -958 -819 + -418 -278 -418 -279 +/* UA.UG..UA */ + -1168 -1028 -1168 -1029 + -478 -338 -478 -339 + -1168 -1028 -1168 -1029 + -558 -418 -558 -419 +/* UA.UU..UA */ + -868 -728 -868 -729 + -458 -318 -458 -319 + -958 -818 -958 -819 + -419 -279 -419 -280 + +# hairpin + INF INF INF 475 532 524 499 503 485 540 + 551 562 571 580 588 595 602 609 615 621 + 626 631 636 641 646 650 654 659 662 666 + 670 + +# hairpin_enthalpies + INF INF INF 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 + 0 + +# bulge + INF 311 203 266 354 327 340 357 371 384 + 395 405 415 423 431 439 446 452 459 464 + 470 475 480 485 490 494 498 502 506 510 + 514 + +# bulge_enthalpies + INF 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 + 0 + +# interior + INF INF INF INF 70 119 100 117 131 144 + 155 165 175 183 191 199 206 212 219 224 + 230 235 240 245 250 254 258 262 266 270 + 274 + +# interior_enthalpies + INF INF INF INF 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 + 0 + +# NINIO +/* Ninio = MIN(max, m*|n1-n2| */ +/* m m_dH max */ + 50 0 300 + +# ML_params +/* F = cu*n_unpaired + cc + ci*loop_degree (+TermAU) */ +/* cu cu_dH cc cc_dH ci ci_dH */ + 4 0 440 0 3 0 + +# Misc +/* all parameters are pairs of 'energy enthalpy' */ +/* DuplexInit TerminalAU LXC */ + 410 0 11 0 107.856000 0 + +# Triloops + +# Tetraloops + GGGGAC 151 -1110 + GGUGAC 50 -1110 + CGAAAG 147 -1340 + GGAGAC 151 -1110 + CGCAAG 147 -1340 + GGAAAC 151 -1110 + CGGAAG 147 -1340 + CUUCGG 52 -1210 + CGUGAG 147 -1340 + CGAAGG 165 -1340 + CUACGG 102 -1210 + GGCAAC 60 -1110 + CGCGAG 170 -1340 + UGAGAG 75 -1060 + CGAGAG 247 -1340 + AGAAAU 202 -740 + CGUAAG 211 -1340 + CUAACG 227 -1140 + UGAAAG 278 -1060 + GGAAGC 228 -1020 + GGGAAC 301 -1110 + UGAAAA 320 -780 + AGCAAU 272 -740 + AGUAAU 201 -740 + CGGGAG 261 -1340 + AGUGAU 72 -740 + GGCGAC 101 -1110 + GGGAGC 294 -1020 + GUGAAC 358 -900 + UGGAAA 328 -780 + +# Hexaloops + + +# END diff --git a/src/energy_params/rna_turner1999.par b/src/energy_params/rna_turner1999.par new file mode 100644 index 0000000..de242e4 --- /dev/null +++ b/src/energy_params/rna_turner1999.par @@ -0,0 +1,9899 @@ +## RNAfold parameter file v2.0 + +# stack +/* CG GC GU UG AU UA @ */ + -240 -330 -210 -140 -210 -210 0 + -330 -340 -250 -150 -220 -240 0 + -210 -250 130 DEF -140 -130 0 + -140 -150 DEF 30 -60 -100 0 + -210 -220 -140 -60 -110 -90 0 + -210 -240 -130 -100 -90 -130 0 + 0 0 0 0 0 0 0 + +# stack_enthalpies +/* CG GC GU UG AU UA @ */ + -1060 -1340 -1210 -560 -1050 -1040 0 + -1340 -1490 -1260 -830 -1140 -1240 0 + -1210 -1260 -1460 -1350 -880 -1280 0 + -560 -830 -1350 -930 -320 -700 0 + -1050 -1140 -880 -320 -940 -680 0 + -1040 -1240 -1280 -700 -680 -770 0 + 0 0 0 0 0 0 0 + +# mismatch_hairpin + 0 0 0 0 0 + -90 -150 -150 -140 -180 + -90 -100 -90 -290 -80 + -90 -220 -200 -160 -110 + -90 -170 -140 -180 -200 + 0 0 0 0 0 + -70 -110 -150 -130 -210 + -70 -110 -70 -240 DEF + -70 -240 -290 -140 -120 + -70 -190 -100 -220 -150 + 0 0 0 0 0 + 0 20 DEF -30 -30 + 0 -10 -20 -150 -20 + 0 -90 -110 -30 0 + 0 -30 -30 -40 -110 + 0 0 0 0 0 + 0 DEF -30 -60 DEF + 0 -20 -10 -170 0 + 0 -80 -120 -30 -70 + 0 -60 -10 -60 -80 + 0 0 0 0 0 + 0 -30 DEF -30 -30 + 0 -10 -20 -150 -20 + 0 -110 -120 -20 20 + 0 -30 -30 -60 -110 + 0 0 0 0 0 + 0 DEF -30 -60 DEF + 0 -20 -10 -120 0 + 0 -140 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-110 -200 -150 + 0 -170 -80 -170 -120 + 0 -170 -80 -170 -120 + 0 -70 -10 -70 -10 + -30 -100 -40 -100 -40 + -30 -100 -40 -100 -40 + -40 -110 DEF -110 DEF + -20 -90 -30 -90 -30 + 0 -80 DEF -80 -60 + -30 -110 -80 -110 -90 + -10 -90 -60 -90 -70 + -20 -100 -70 -100 -80 + -20 -100 -70 -100 -80 + 0 -70 -10 -70 -10 + -30 -100 -40 -100 -40 + -30 -100 -40 -100 -40 + -40 -110 DEF -110 DEF + -20 -90 -30 -90 -30 + 0 -80 DEF -80 -60 + -30 -110 -80 -110 -90 + -10 -90 -60 -90 -70 + -20 -100 -70 -100 -80 + -20 -100 -70 -100 -80 + 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 + +# mismatch_exterior_enthalpies +/* @ A C G U */ + 0 -740 -280 -640 -360 + -240 -980 -520 -880 -600 + 330 -410 50 -310 -30 + 80 -660 -200 -560 -280 + -140 -880 -420 -780 -500 + 0 -900 -410 -860 -750 + -160 -1060 -570 -1020 -910 + 70 -830 -340 -790 -680 + -460 -1360 -870 -1320 -1210 + -40 -940 -450 -900 -790 + 0 -740 -240 -720 -490 + 160 -580 -80 -560 -330 + 220 -520 -20 -500 -270 + 70 -670 -170 -650 -420 + 310 -430 70 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550 550 + 550 550 550 550 550 +/* UA.A..CG */ + 550 550 550 550 550 + 550 320 300 240 480 + 550 290 250 240 480 + 550 180 140 120 480 + 550 480 480 480 480 +/* UA.C..CG */ + 550 550 550 550 550 + 550 310 300 480 300 + 550 300 330 480 300 + 550 480 480 480 480 + 550 330 270 480 300 +/* UA.G..CG */ + 550 550 550 550 550 + 550 250 480 160 480 + 550 480 480 480 480 + 550 160 480 300 480 + 550 480 480 480 480 +/* UA.U..CG */ + 550 550 550 550 550 + 550 480 480 480 480 + 550 480 300 480 210 + 550 480 480 480 480 + 550 480 250 480 200 +/* UA.@..GC */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* UA.A..GC */ + 550 550 550 550 550 + 550 320 300 240 480 + 550 290 250 240 480 + 550 180 140 120 480 + 550 480 480 480 480 +/* UA.C..GC */ + 550 550 550 550 550 + 550 310 300 480 300 + 550 300 330 480 300 + 550 480 480 480 480 + 550 330 270 480 300 +/* UA.G..GC */ + 550 550 550 550 550 + 550 250 480 160 480 + 550 480 480 480 480 + 550 160 480 300 480 + 550 480 480 480 480 +/* UA.U..GC */ + 550 550 550 550 550 + 550 480 480 480 480 + 550 480 300 480 210 + 550 480 480 480 480 + 550 480 250 480 200 +/* UA.@..GU */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* UA.A..GU */ + 550 550 550 550 550 + 550 390 370 310 550 + 550 360 320 310 550 + 550 250 210 190 550 + 550 550 550 550 550 +/* UA.C..GU */ + 550 550 550 550 550 + 550 380 370 550 370 + 550 370 400 550 370 + 550 550 550 550 550 + 550 400 340 550 370 +/* UA.G..GU */ + 550 550 550 550 550 + 550 320 550 230 550 + 550 550 550 550 550 + 550 230 550 370 550 + 550 550 550 550 550 +/* UA.U..GU */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 370 550 280 + 550 550 550 550 550 + 550 550 320 550 270 +/* UA.@..UG */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* UA.A..UG */ + 550 550 550 550 550 + 550 390 370 310 550 + 550 360 320 310 550 + 550 250 210 190 550 + 550 550 550 550 550 +/* UA.C..UG */ + 550 550 550 550 550 + 550 380 370 550 370 + 550 370 400 550 370 + 550 550 550 550 550 + 550 400 340 550 370 +/* UA.G..UG */ + 550 550 550 550 550 + 550 320 550 230 550 + 550 550 550 550 550 + 550 230 550 370 550 + 550 550 550 550 550 +/* UA.U..UG */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 370 550 280 + 550 550 550 550 550 + 550 550 320 550 270 +/* UA.@..AU */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* UA.A..AU */ + 550 550 550 550 550 + 550 390 370 310 550 + 550 360 320 310 550 + 550 250 210 190 550 + 550 550 550 550 550 +/* UA.C..AU */ + 550 550 550 550 550 + 550 380 370 550 370 + 550 370 400 550 370 + 550 550 550 550 550 + 550 400 340 550 370 +/* UA.G..AU */ + 550 550 550 550 550 + 550 320 550 230 550 + 550 550 550 550 550 + 550 230 550 370 550 + 550 550 550 550 550 +/* UA.U..AU */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 370 550 280 + 550 550 550 550 550 + 550 550 320 550 270 +/* UA.@..UA */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* UA.A..UA */ + 550 550 550 550 550 + 550 390 370 310 550 + 550 360 320 310 550 + 550 250 210 190 550 + 550 550 550 550 550 +/* UA.C..UA */ + 550 550 550 550 550 + 550 380 370 550 370 + 550 370 400 550 370 + 550 550 550 550 550 + 550 400 340 550 370 +/* UA.G..UA */ + 550 550 550 550 550 + 550 320 550 230 550 + 550 550 550 550 550 + 550 230 550 370 550 + 550 550 550 550 550 +/* UA.U..UA */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 370 550 280 + 550 550 550 550 550 + 550 550 320 550 270 +/* UA.@.. @ */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* UA.A.. @ */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* UA.C.. @ */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* UA.G.. @ */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* UA.U.. @ */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.@..CG */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.A..CG */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.C..CG */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.G..CG */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.U..CG */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.@..GC */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.A..GC */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.C..GC */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.G..GC */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.U..GC */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.@..GU */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.A..GU */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.C..GU */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.G..GU */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.U..GU */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.@..UG */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.A..UG */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.C..UG */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.G..UG */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.U..UG */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.@..AU */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.A..AU */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.C..AU */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.G..AU */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.U..AU */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.@..UA */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.A..UA */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.C..UA */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.G..UA */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.U..UA */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.@.. @ */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.A.. @ */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.C.. @ */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.G.. @ */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 +/* @.U.. @ */ + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + 550 550 550 550 550 + +# int21_enthalpies +/* CG.@..CG */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* CG.A..CG */ + DEF -1029 -949 -1029 -1029 + -1079 -2058 -1978 -2058 -2058 + -569 -1548 -1468 -1548 -1548 + -989 -1968 -1888 -1968 -1968 + -859 -1838 -1758 -1838 -1838 +/* CG.C..CG */ + DEF -519 -449 -519 -669 + -999 -1468 -1398 -1468 -1618 + -499 -968 -898 -968 -1118 + -989 -1458 -1388 -1458 -1608 + -789 -1258 -1188 -1258 -1408 +/* CG.G..CG */ + DEF -939 -939 -939 -939 + -1079 -1968 -1968 -1968 -1968 + -569 -1458 -1458 -1458 -1458 + -989 -1878 -1878 -1878 -1878 + -859 -1748 -1748 -1748 -1748 +/* CG.U..CG */ + DEF -809 -739 -809 -859 + -1079 -1838 -1768 -1838 -1888 + -719 -1478 -1408 -1478 -1528 + -989 -1748 -1678 -1748 -1798 + -909 -1668 -1598 -1668 -1718 +/* CG.@..GC */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* CG.A..GC */ + DEF -1029 -949 -1029 -1029 + -569 -1548 -1468 -1548 -1548 + -769 -1748 -1668 -1748 -1748 + -759 -1738 -1658 -1738 -1738 + -549 -1528 -1448 -1528 -1528 +/* CG.C..GC */ + DEF -519 -449 -519 -669 + -929 -1398 -1328 -1398 -1548 + -359 -828 -758 -828 -978 + -789 -1258 -1188 -1258 -1408 + -549 -1018 -948 -1018 -1168 +/* CG.G..GC */ + DEF -939 -939 -939 -939 + -609 -1498 -1498 -1498 -1498 + -359 -1248 -1248 -1248 -1248 + -669 -1558 -1558 -1558 -1558 + -549 -1438 -1438 -1438 -1438 +/* CG.U..GC */ + DEF -809 -739 -809 -859 + -929 -1688 -1618 -1688 -1738 + -439 -1198 -1128 -1198 -1248 + -789 -1548 -1478 -1548 -1598 + -619 -1378 -1308 -1378 -1428 +/* CG.@..GU */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* CG.A..GU */ + DEF -1029 -949 -1029 -1029 + -479 -1458 -1378 -1458 -1458 + -309 -1288 -1208 -1288 -1288 + -389 -1368 -1288 -1368 -1368 + -379 -1358 -1278 -1358 -1358 +/* CG.C..GU */ + DEF -519 -449 -519 -669 + -649 -1118 -1048 -1118 -1268 + -289 -758 -688 -758 -908 + -739 -1208 -1138 -1208 -1358 + -379 -848 -778 -848 -998 +/* CG.G..GU */ + DEF -939 -939 -939 -939 + -649 -1538 -1538 -1538 -1538 + -289 -1178 -1178 -1178 -1178 + -739 -1628 -1628 -1628 -1628 + -379 -1268 -1268 -1268 -1268 +/* CG.U..GU */ + DEF -809 -739 -809 -859 + -649 -1408 -1338 -1408 -1458 + -289 -1048 -978 -1048 -1098 + -739 -1498 -1428 -1498 -1548 + -379 -1138 -1068 -1138 -1188 +/* CG.@..UG */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* CG.A..UG */ + DEF -1029 -949 -1029 -1029 + -769 -1748 -1668 -1748 -1748 + -529 -1508 -1428 -1508 -1508 + -709 -1688 -1608 -1688 -1688 + -599 -1578 -1498 -1578 -1578 +/* CG.C..UG */ + DEF -519 -449 -519 -669 + -839 -1308 -1238 -1308 -1458 + -529 -998 -928 -998 -1148 + -859 -1328 -1258 -1328 -1478 + -489 -958 -888 -958 -1108 +/* CG.G..UG */ + DEF -939 -939 -939 -939 + -1009 -1898 -1898 -1898 -1898 + -409 -1298 -1298 -1298 -1298 + -969 -1858 -1858 -1858 -1858 + -599 -1488 -1488 -1488 -1488 +/* CG.U..UG */ + DEF -809 -739 -809 -859 + -859 -1618 -1548 -1618 -1668 + -529 -1288 -1218 -1288 -1338 + -859 -1618 -1548 -1618 -1668 + -409 -1168 -1098 -1168 -1218 +/* CG.@..AU */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* CG.A..AU */ + DEF -1029 -949 -1029 -1029 + -479 -1458 -1378 -1458 -1458 + -309 -1288 -1208 -1288 -1288 + -389 -1368 -1288 -1368 -1368 + -379 -1358 -1278 -1358 -1358 +/* CG.C..AU */ + DEF -519 -449 -519 -669 + -649 -1118 -1048 -1118 -1268 + -289 -758 -688 -758 -908 + -739 -1208 -1138 -1208 -1358 + -379 -848 -778 -848 -998 +/* CG.G..AU */ + DEF -939 -939 -939 -939 + -649 -1538 -1538 -1538 -1538 + -289 -1178 -1178 -1178 -1178 + -739 -1628 -1628 -1628 -1628 + -379 -1268 -1268 -1268 -1268 +/* CG.U..AU */ + DEF -809 -739 -809 -859 + -649 -1408 -1338 -1408 -1458 + -289 -1048 -978 -1048 -1098 + -739 -1498 -1428 -1498 -1548 + -379 -1138 -1068 -1138 -1188 +/* CG.@..UA */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* CG.A..UA */ + DEF -1029 -949 -1029 -1029 + -449 -1428 -1348 -1428 -1428 + -479 -1458 -1378 -1458 -1458 + -429 -1408 -1328 -1408 -1408 + -329 -1308 -1228 -1308 -1308 +/* CG.C..UA */ + DEF -519 -449 -519 -669 + -679 -1148 -1078 -1148 -1298 + -559 -1028 -958 -1028 -1178 + -729 -1198 -1128 -1198 -1348 + -189 -658 -588 -658 -808 +/* CG.G..UA */ + DEF -939 -939 -939 -939 + -939 -1828 -1828 -1828 -1828 + -249 -1138 -1138 -1138 -1138 + -939 -1828 -1828 -1828 -1828 + -329 -1218 -1218 -1218 -1218 +/* CG.U..UA */ + DEF -809 -739 -809 -859 + -639 -1398 -1328 -1398 -1448 + -229 -988 -918 -988 -1038 + -729 -1488 -1418 -1488 -1538 + -190 -949 -879 -949 -999 +/* CG.@.. @ */ + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* CG.A.. @ */ + -100 -1079 -999 -1079 -1079 + -100 -1079 -999 -1079 -1079 + -100 -1079 -999 -1079 -1079 + -100 -1079 -999 -1079 -1079 + -100 -1079 -999 -1079 -1079 +/* CG.C.. @ */ + -100 -569 -499 -569 -719 + -100 -569 -499 -569 -719 + -100 -569 -499 -569 -719 + -100 -569 -499 -569 -719 + -100 -569 -499 -569 -719 +/* CG.G.. @ */ + -100 -989 -989 -989 -989 + -100 -989 -989 -989 -989 + -100 -989 -989 -989 -989 + -100 -989 -989 -989 -989 + -100 -989 -989 -989 -989 +/* CG.U.. @ */ + -100 -859 -789 -859 -909 + -100 -859 -789 -859 -909 + -100 -859 -789 -859 -909 + -100 -859 -789 -859 -909 + -100 -859 -789 -859 -909 +/* GC.@..CG */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* GC.A..CG */ + DEF -519 -879 -559 -879 + -1079 -1548 -1908 -1588 -1908 + -569 -1038 -1398 -1078 -1398 + -989 -1458 -1818 -1498 -1818 + -859 -1328 -1688 -1368 -1688 +/* GC.C..CG */ + DEF -719 -309 -309 -389 + -999 -1668 -1258 -1258 -1338 + -499 -1168 -758 -758 -838 + -989 -1658 -1248 -1248 -1328 + -789 -1458 -1048 -1048 -1128 +/* GC.G..CG */ + DEF -709 -739 -619 -739 + -1079 -1738 -1768 -1648 -1768 + -569 -1228 -1258 -1138 -1258 + -989 -1648 -1678 -1558 -1678 + -859 -1518 -1548 -1428 -1548 +/* GC.U..CG */ + DEF -499 -499 -499 -569 + -1079 -1528 -1528 -1528 -1598 + -719 -1168 -1168 -1168 -1238 + -989 -1438 -1438 -1438 -1508 + -909 -1358 -1358 -1358 -1428 +/* GC.@..GC */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* GC.A..GC */ + DEF -519 -879 -559 -879 + -569 -1038 -1398 -1078 -1398 + -769 -1238 -1598 -1278 -1598 + -759 -1228 -1588 -1268 -1588 + -549 -1018 -1378 -1058 -1378 +/* GC.C..GC */ + DEF -719 -309 -309 -389 + -929 -1598 -1188 -1188 -1268 + -359 -1028 -618 -618 -698 + -789 -1458 -1048 -1048 -1128 + -549 -1218 -808 -808 -888 +/* GC.G..GC */ + DEF -709 -739 -619 -739 + -609 -1268 -1298 -1178 -1298 + -359 -1018 -1048 -928 -1048 + -669 -1328 -1358 -1238 -1358 + -549 -1208 -1238 -1118 -1238 +/* GC.U..GC */ + DEF -499 -499 -499 -569 + -929 -1378 -1378 -1378 -1448 + -439 -888 -888 -888 -958 + -789 -1238 -1238 -1238 -1308 + -619 -1068 -1068 -1068 -1138 +/* GC.@..GU */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* GC.A..GU */ + DEF -519 -879 -559 -879 + -479 -948 -1308 -988 -1308 + -309 -778 -1138 -818 -1138 + -389 -858 -1218 -898 -1218 + -379 -848 -1208 -888 -1208 +/* GC.C..GU */ + DEF -719 -309 -309 -389 + -649 -1318 -908 -908 -988 + -289 -958 -548 -548 -628 + -739 -1408 -998 -998 -1078 + -379 -1048 -638 -638 -718 +/* GC.G..GU */ + DEF -709 -739 -619 -739 + -649 -1308 -1338 -1218 -1338 + -289 -948 -978 -858 -978 + -739 -1398 -1428 -1308 -1428 + -379 -1038 -1068 -948 -1068 +/* GC.U..GU */ + DEF -499 -499 -499 -569 + -649 -1098 -1098 -1098 -1168 + -289 -738 -738 -738 -808 + -739 -1188 -1188 -1188 -1258 + -379 -828 -828 -828 -898 +/* GC.@..UG */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* GC.A..UG */ + DEF -519 -879 -559 -879 + -769 -1238 -1598 -1278 -1598 + -529 -998 -1358 -1038 -1358 + -709 -1178 -1538 -1218 -1538 + -599 -1068 -1428 -1108 -1428 +/* GC.C..UG */ + DEF -719 -309 -309 -389 + -839 -1508 -1098 -1098 -1178 + -529 -1198 -788 -788 -868 + -859 -1528 -1118 -1118 -1198 + -489 -1158 -748 -748 -828 +/* GC.G..UG */ + DEF -709 -739 -619 -739 + -1009 -1668 -1698 -1578 -1698 + -409 -1068 -1098 -978 -1098 + -969 -1628 -1658 -1538 -1658 + -599 -1258 -1288 -1168 -1288 +/* GC.U..UG */ + DEF -499 -499 -499 -569 + -859 -1308 -1308 -1308 -1378 + -529 -978 -978 -978 -1048 + -859 -1308 -1308 -1308 -1378 + -409 -858 -858 -858 -928 +/* GC.@..AU */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* GC.A..AU */ + DEF -519 -879 -559 -879 + -479 -948 -1308 -988 -1308 + -309 -778 -1138 -818 -1138 + -389 -858 -1218 -898 -1218 + -379 -848 -1208 -888 -1208 +/* GC.C..AU */ + DEF -719 -309 -309 -389 + -649 -1318 -908 -908 -988 + -289 -958 -548 -548 -628 + -739 -1408 -998 -998 -1078 + -379 -1048 -638 -638 -718 +/* GC.G..AU */ + DEF -709 -739 -619 -739 + -649 -1308 -1338 -1218 -1338 + -289 -948 -978 -858 -978 + -739 -1398 -1428 -1308 -1428 + -379 -1038 -1068 -948 -1068 +/* GC.U..AU */ + DEF -499 -499 -499 -569 + -649 -1098 -1098 -1098 -1168 + -289 -738 -738 -738 -808 + -739 -1188 -1188 -1188 -1258 + -379 -828 -828 -828 -898 +/* GC.@..UA */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* GC.A..UA */ + DEF -519 -879 -559 -879 + -449 -918 -1278 -958 -1278 + -479 -948 -1308 -988 -1308 + -429 -898 -1258 -938 -1258 + -329 -798 -1158 -838 -1158 +/* GC.C..UA */ + DEF -719 -309 -309 -389 + -679 -1348 -938 -938 -1018 + -559 -1228 -818 -818 -898 + -729 -1398 -988 -988 -1068 + -189 -858 -448 -448 -528 +/* GC.G..UA */ + DEF -709 -739 -619 -739 + -939 -1598 -1628 -1508 -1628 + -249 -908 -938 -818 -938 + -939 -1598 -1628 -1508 -1628 + -329 -988 -1018 -898 -1018 +/* GC.U..UA */ + DEF -499 -499 -499 -569 + -639 -1088 -1088 -1088 -1158 + -229 -678 -678 -678 -748 + -729 -1178 -1178 -1178 -1248 + -190 -639 -639 -639 -709 +/* GC.@.. @ */ + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* GC.A.. @ */ + -100 -569 -929 -609 -929 + -100 -569 -929 -609 -929 + -100 -569 -929 -609 -929 + -100 -569 -929 -609 -929 + -100 -569 -929 -609 -929 +/* GC.C.. @ */ + -100 -769 -359 -359 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DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* UG.A..UG */ + DEF -719 -789 -959 -809 + -769 -1438 -1508 -1678 -1528 + -529 -1198 -1268 -1438 -1288 + -709 -1378 -1448 -1618 -1468 + -599 -1268 -1338 -1508 -1358 +/* UG.C..UG */ + DEF -479 -479 -359 -479 + -839 -1268 -1268 -1148 -1268 + -529 -958 -958 -838 -958 + -859 -1288 -1288 -1168 -1288 + -489 -918 -918 -798 -918 +/* UG.G..UG */ + DEF -659 -809 -919 -809 + -1009 -1618 -1768 -1878 -1768 + -409 -1018 -1168 -1278 -1168 + -969 -1578 -1728 -1838 -1728 + -599 -1208 -1358 -1468 -1358 +/* UG.U..UG */ + DEF -549 -439 -549 -359 + -859 -1358 -1248 -1358 -1168 + -529 -1028 -918 -1028 -838 + -859 -1358 -1248 -1358 -1168 + -409 -908 -798 -908 -718 +/* UG.@..AU */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* UG.A..AU */ + DEF -719 -789 -959 -809 + -479 -1148 -1218 -1388 -1238 + -309 -978 -1048 -1218 -1068 + -389 -1058 -1128 -1298 -1148 + -379 -1048 -1118 -1288 -1138 +/* 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-1008 -1118 -1008 + -939 -1548 -1698 -1808 -1698 + -329 -938 -1088 -1198 -1088 +/* UG.U..UA */ + DEF -549 -439 -549 -359 + -639 -1138 -1028 -1138 -948 + -229 -728 -618 -728 -538 + -729 -1228 -1118 -1228 -1038 + -190 -689 -579 -689 -499 +/* UG.@.. @ */ + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* UG.A.. @ */ + -100 -769 -839 -1009 -859 + -100 -769 -839 -1009 -859 + -100 -769 -839 -1009 -859 + -100 -769 -839 -1009 -859 + -100 -769 -839 -1009 -859 +/* UG.C.. @ */ + -100 -529 -529 -409 -529 + -100 -529 -529 -409 -529 + -100 -529 -529 -409 -529 + -100 -529 -529 -409 -529 + -100 -529 -529 -409 -529 +/* UG.G.. @ */ + -100 -709 -859 -969 -859 + -100 -709 -859 -969 -859 + -100 -709 -859 -969 -859 + -100 -709 -859 -969 -859 + -100 -709 -859 -969 -859 +/* UG.U.. @ */ + -100 -599 -489 -599 -409 + -100 -599 -489 -599 -409 + -100 -599 -489 -599 -409 + -100 -599 -489 -599 -409 + -100 -599 -489 -599 -409 +/* AU.@..CG */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* AU.A..CG */ + DEF -429 -599 -599 -599 + -1079 -1458 -1628 -1628 -1628 + -569 -948 -1118 -1118 -1118 + -989 -1368 -1538 -1538 -1538 + -859 -1238 -1408 -1408 -1408 +/* AU.C..CG */ + DEF -259 -239 -239 -239 + -999 -1208 -1188 -1188 -1188 + -499 -708 -688 -688 -688 + -989 -1198 -1178 -1178 -1178 + -789 -998 -978 -978 -978 +/* AU.G..CG */ + DEF -339 -689 -689 -689 + -1079 -1368 -1718 -1718 -1718 + -569 -858 -1208 -1208 -1208 + -989 -1278 -1628 -1628 -1628 + -859 -1148 -1498 -1498 -1498 +/* AU.U..CG */ + DEF -329 -329 -329 -329 + -1079 -1358 -1358 -1358 -1358 + -719 -998 -998 -998 -998 + -989 -1268 -1268 -1268 -1268 + -909 -1188 -1188 -1188 -1188 +/* AU.@..GC */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* AU.A..GC */ + DEF -429 -599 -599 -599 + -569 -948 -1118 -1118 -1118 + -769 -1148 -1318 -1318 -1318 + -759 -1138 -1308 -1308 -1308 + -549 -928 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*/ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* AU.A..AU */ + DEF -429 -599 -599 -599 + -479 -858 -1028 -1028 -1028 + -309 -688 -858 -858 -858 + -389 -768 -938 -938 -938 + -379 -758 -928 -928 -928 +/* AU.C..AU */ + DEF -259 -239 -239 -239 + -649 -858 -838 -838 -838 + -289 -498 -478 -478 -478 + -739 -948 -928 -928 -928 + -379 -588 -568 -568 -568 +/* AU.G..AU */ + DEF -339 -689 -689 -689 + -649 -938 -1288 -1288 -1288 + -289 -578 -928 -928 -928 + -739 -1028 -1378 -1378 -1378 + -379 -668 -1018 -1018 -1018 +/* AU.U..AU */ + DEF -329 -329 -329 -329 + -649 -928 -928 -928 -928 + -289 -568 -568 -568 -568 + -739 -1018 -1018 -1018 -1018 + -379 -658 -658 -658 -658 +/* AU.@..UA */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* AU.A..UA */ + DEF -429 -599 -599 -599 + -449 -828 -998 -998 -998 + -479 -858 -1028 -1028 -1028 + -429 -808 -978 -978 -978 + -329 -708 -878 -878 -878 +/* AU.C..UA */ + DEF -259 -239 -239 -239 + -679 -888 -868 -868 -868 + -559 -768 -748 -748 -748 + -729 -938 -918 -918 -918 + -189 -398 -378 -378 -378 +/* AU.G..UA */ + DEF -339 -689 -689 -689 + -939 -1228 -1578 -1578 -1578 + -249 -538 -888 -888 -888 + -939 -1228 -1578 -1578 -1578 + -329 -618 -968 -968 -968 +/* AU.U..UA */ + DEF -329 -329 -329 -329 + -639 -918 -918 -918 -918 + -229 -508 -508 -508 -508 + -729 -1008 -1008 -1008 -1008 + -190 -469 -469 -469 -469 +/* AU.@.. @ */ + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* AU.A.. @ */ + -100 -479 -649 -649 -649 + -100 -479 -649 -649 -649 + -100 -479 -649 -649 -649 + -100 -479 -649 -649 -649 + -100 -479 -649 -649 -649 +/* AU.C.. @ */ + -100 -309 -289 -289 -289 + -100 -309 -289 -289 -289 + -100 -309 -289 -289 -289 + -100 -309 -289 -289 -289 + -100 -309 -289 -289 -289 +/* AU.G.. @ */ + -100 -389 -739 -739 -739 + -100 -389 -739 -739 -739 + -100 -389 -739 -739 -739 + -100 -389 -739 -739 -739 + -100 -389 -739 -739 -739 +/* AU.U.. @ */ + -100 -379 -379 -379 -379 + -100 -379 -379 -379 -379 + -100 -379 -379 -379 -379 + -100 -379 -379 -379 -379 + -100 -379 -379 -379 -379 +/* UA.@..CG */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* UA.A..CG */ + DEF -399 -629 -889 -589 + -1079 -1428 -1658 -1918 -1618 + -569 -918 -1148 -1408 -1108 + -989 -1338 -1568 -1828 -1528 + -859 -1208 -1438 -1698 -1398 +/* UA.C..CG */ + DEF -429 -509 -199 -179 + -999 -1378 -1458 -1148 -1128 + -499 -878 -958 -648 -628 + -989 -1368 -1448 -1138 -1118 + -789 -1168 -1248 -938 -918 +/* UA.G..CG */ + DEF -379 -679 -889 -679 + -1079 -1408 -1708 -1918 -1708 + -569 -898 -1198 -1408 -1198 + -989 -1318 -1618 -1828 -1618 + -859 -1188 -1488 -1698 -1488 +/* UA.U..CG */ + DEF -279 -139 -279 -140 + -1079 -1308 -1168 -1308 -1169 + -719 -948 -808 -948 -809 + -989 -1218 -1078 -1218 -1079 + -909 -1138 -998 -1138 -999 +/* UA.@..GC */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* UA.A..GC */ + DEF -399 -629 -889 -589 + -569 -918 -1148 -1408 -1108 + -769 -1118 -1348 -1608 -1308 + -759 -1108 -1338 -1598 -1298 + -549 -898 -1128 -1388 -1088 +/* UA.C..GC */ + DEF -429 -509 -199 -179 + -929 -1308 -1388 -1078 -1058 + -359 -738 -818 -508 -488 + -789 -1168 -1248 -938 -918 + -549 -928 -1008 -698 -678 +/* UA.G..GC */ + DEF -379 -679 -889 -679 + -609 -938 -1238 -1448 -1238 + -359 -688 -988 -1198 -988 + -669 -998 -1298 -1508 -1298 + -549 -878 -1178 -1388 -1178 +/* UA.U..GC */ + DEF -279 -139 -279 -140 + -929 -1158 -1018 -1158 -1019 + -439 -668 -528 -668 -529 + -789 -1018 -878 -1018 -879 + -619 -848 -708 -848 -709 +/* UA.@..GU */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* UA.A..GU */ + DEF -399 -629 -889 -589 + -479 -828 -1058 -1318 -1018 + -309 -658 -888 -1148 -848 + -389 -738 -968 -1228 -928 + -379 -728 -958 -1218 -918 +/* UA.C..GU */ + DEF -429 -509 -199 -179 + -649 -1028 -1108 -798 -778 + -289 -668 -748 -438 -418 + -739 -1118 -1198 -888 -868 + -379 -758 -838 -528 -508 +/* UA.G..GU */ + DEF -379 -679 -889 -679 + -649 -978 -1278 -1488 -1278 + -289 -618 -918 -1128 -918 + -739 -1068 -1368 -1578 -1368 + -379 -708 -1008 -1218 -1008 +/* UA.U..GU */ + DEF -279 -139 -279 -140 + -649 -878 -738 -878 -739 + -289 -518 -378 -518 -379 + -739 -968 -828 -968 -829 + -379 -608 -468 -608 -469 +/* UA.@..UG */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* UA.A..UG */ + DEF -399 -629 -889 -589 + -769 -1118 -1348 -1608 -1308 + -529 -878 -1108 -1368 -1068 + -709 -1058 -1288 -1548 -1248 + -599 -948 -1178 -1438 -1138 +/* UA.C..UG */ + DEF -429 -509 -199 -179 + -839 -1218 -1298 -988 -968 + -529 -908 -988 -678 -658 + -859 -1238 -1318 -1008 -988 + -489 -868 -948 -638 -618 +/* UA.G..UG */ + DEF -379 -679 -889 -679 + -1009 -1338 -1638 -1848 -1638 + -409 -738 -1038 -1248 -1038 + -969 -1298 -1598 -1808 -1598 + -599 -928 -1228 -1438 -1228 +/* UA.U..UG */ + DEF -279 -139 -279 -140 + -859 -1088 -948 -1088 -949 + -529 -758 -618 -758 -619 + -859 -1088 -948 -1088 -949 + -409 -638 -498 -638 -499 +/* UA.@..AU */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* UA.A..AU */ + DEF -399 -629 -889 -589 + -479 -828 -1058 -1318 -1018 + -309 -658 -888 -1148 -848 + -389 -738 -968 -1228 -928 + -379 -728 -958 -1218 -918 +/* UA.C..AU */ + DEF -429 -509 -199 -179 + -649 -1028 -1108 -798 -778 + -289 -668 -748 -438 -418 + -739 -1118 -1198 -888 -868 + -379 -758 -838 -528 -508 +/* UA.G..AU */ + DEF -379 -679 -889 -679 + -649 -978 -1278 -1488 -1278 + -289 -618 -918 -1128 -918 + -739 -1068 -1368 -1578 -1368 + -379 -708 -1008 -1218 -1008 +/* UA.U..AU */ + DEF -279 -139 -279 -140 + -649 -878 -738 -878 -739 + -289 -518 -378 -518 -379 + -739 -968 -828 -968 -829 + -379 -608 -468 -608 -469 +/* UA.@..UA */ + 0 0 0 0 0 + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* UA.A..UA */ + DEF -399 -629 -889 -589 + -449 -798 -1028 -1288 -988 + -479 -828 -1058 -1318 -1018 + -429 -778 -1008 -1268 -968 + -329 -678 -908 -1168 -868 +/* UA.C..UA */ + DEF -429 -509 -199 -179 + -679 -1058 -1138 -828 -808 + -559 -938 -1018 -708 -688 + -729 -1108 -1188 -878 -858 + -189 -568 -648 -338 -318 +/* UA.G..UA */ + DEF -379 -679 -889 -679 + -939 -1268 -1568 -1778 -1568 + -249 -578 -878 -1088 -878 + -939 -1268 -1568 -1778 -1568 + -329 -658 -958 -1168 -958 +/* UA.U..UA */ + DEF -279 -139 -279 -140 + -639 -868 -728 -868 -729 + -229 -458 -318 -458 -319 + -729 -958 -818 -958 -819 + -190 -419 -279 -419 -280 +/* UA.@.. @ */ + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF + DEF DEF DEF DEF DEF +/* UA.A.. @ */ + -100 -449 -679 -939 -639 + -100 -449 -679 -939 -639 + -100 -449 -679 -939 -639 + -100 -449 -679 -939 -639 + -100 -449 -679 -939 -639 +/* UA.C.. @ */ + -100 -479 -559 -249 -229 + -100 -479 -559 -249 -229 + -100 -479 -559 -249 -229 + -100 -479 -559 -249 -229 + -100 -479 -559 -249 -229 +/* UA.G.. @ */ + -100 -429 -729 -939 -729 + -100 -429 -729 -939 -729 + -100 -429 -729 -939 -729 + -100 -429 -729 -939 -729 + -100 -429 -729 -939 -729 +/* UA.U.. @ */ + -100 -329 -189 -329 -190 + -100 -329 -189 -329 -190 + -100 -329 -189 -329 -190 + -100 -329 -189 -329 -190 + -100 -329 -189 -329 -190 +/* @.@..CG */ + DEF DEF DEF DEF DEF + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.A..CG */ + DEF DEF DEF DEF DEF + -1079 -1079 -1079 -1079 -1079 + -569 -569 -569 -569 -569 + -989 -989 -989 -989 -989 + -859 -859 -859 -859 -859 +/* @.C..CG */ + DEF DEF DEF DEF DEF + -999 -999 -999 -999 -999 + -499 -499 -499 -499 -499 + -989 -989 -989 -989 -989 + -789 -789 -789 -789 -789 +/* @.G..CG */ + DEF DEF DEF DEF DEF + -1079 -1079 -1079 -1079 -1079 + -569 -569 -569 -569 -569 + -989 -989 -989 -989 -989 + -859 -859 -859 -859 -859 +/* @.U..CG */ + DEF DEF DEF DEF DEF + -1079 -1079 -1079 -1079 -1079 + -719 -719 -719 -719 -719 + -989 -989 -989 -989 -989 + -909 -909 -909 -909 -909 +/* @.@..GC */ + DEF DEF DEF DEF DEF + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.A..GC */ + DEF DEF DEF DEF DEF + -569 -569 -569 -569 -569 + -769 -769 -769 -769 -769 + -759 -759 -759 -759 -759 + -549 -549 -549 -549 -549 +/* @.C..GC */ + DEF DEF DEF DEF DEF + -929 -929 -929 -929 -929 + -359 -359 -359 -359 -359 + -789 -789 -789 -789 -789 + -549 -549 -549 -549 -549 +/* @.G..GC */ + DEF DEF DEF DEF DEF + -609 -609 -609 -609 -609 + -359 -359 -359 -359 -359 + -669 -669 -669 -669 -669 + -549 -549 -549 -549 -549 +/* @.U..GC */ + DEF DEF DEF DEF DEF + -929 -929 -929 -929 -929 + -439 -439 -439 -439 -439 + -789 -789 -789 -789 -789 + -619 -619 -619 -619 -619 +/* @.@..GU */ + DEF DEF DEF DEF DEF + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.A..GU */ + DEF DEF DEF DEF DEF + -479 -479 -479 -479 -479 + -309 -309 -309 -309 -309 + -389 -389 -389 -389 -389 + -379 -379 -379 -379 -379 +/* @.C..GU */ + DEF DEF DEF DEF DEF + -649 -649 -649 -649 -649 + -289 -289 -289 -289 -289 + -739 -739 -739 -739 -739 + -379 -379 -379 -379 -379 +/* @.G..GU */ + DEF DEF DEF DEF DEF + -649 -649 -649 -649 -649 + -289 -289 -289 -289 -289 + -739 -739 -739 -739 -739 + -379 -379 -379 -379 -379 +/* @.U..GU */ + DEF DEF DEF DEF DEF + -649 -649 -649 -649 -649 + -289 -289 -289 -289 -289 + -739 -739 -739 -739 -739 + -379 -379 -379 -379 -379 +/* @.@..UG */ + DEF DEF DEF DEF DEF + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.A..UG */ + DEF DEF DEF DEF DEF + -769 -769 -769 -769 -769 + -529 -529 -529 -529 -529 + -709 -709 -709 -709 -709 + -599 -599 -599 -599 -599 +/* @.C..UG */ + DEF DEF DEF DEF DEF + -839 -839 -839 -839 -839 + -529 -529 -529 -529 -529 + -859 -859 -859 -859 -859 + -489 -489 -489 -489 -489 +/* @.G..UG */ + DEF DEF DEF DEF DEF + -1009 -1009 -1009 -1009 -1009 + -409 -409 -409 -409 -409 + -969 -969 -969 -969 -969 + -599 -599 -599 -599 -599 +/* @.U..UG */ + DEF DEF DEF DEF DEF + -859 -859 -859 -859 -859 + -529 -529 -529 -529 -529 + -859 -859 -859 -859 -859 + -409 -409 -409 -409 -409 +/* @.@..AU */ + DEF DEF DEF DEF DEF + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.A..AU */ + DEF DEF DEF DEF DEF + -479 -479 -479 -479 -479 + -309 -309 -309 -309 -309 + -389 -389 -389 -389 -389 + -379 -379 -379 -379 -379 +/* @.C..AU */ + DEF DEF DEF DEF DEF + -649 -649 -649 -649 -649 + -289 -289 -289 -289 -289 + -739 -739 -739 -739 -739 + -379 -379 -379 -379 -379 +/* @.G..AU */ + DEF DEF DEF DEF DEF + -649 -649 -649 -649 -649 + -289 -289 -289 -289 -289 + -739 -739 -739 -739 -739 + -379 -379 -379 -379 -379 +/* @.U..AU */ + DEF DEF DEF DEF DEF + -649 -649 -649 -649 -649 + -289 -289 -289 -289 -289 + -739 -739 -739 -739 -739 + -379 -379 -379 -379 -379 +/* @.@..UA */ + DEF DEF DEF DEF DEF + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.A..UA */ + DEF DEF DEF DEF DEF + -449 -449 -449 -449 -449 + -479 -479 -479 -479 -479 + -429 -429 -429 -429 -429 + -329 -329 -329 -329 -329 +/* @.C..UA */ + DEF DEF DEF DEF DEF + -679 -679 -679 -679 -679 + -559 -559 -559 -559 -559 + -729 -729 -729 -729 -729 + -189 -189 -189 -189 -189 +/* @.G..UA */ + DEF DEF DEF DEF DEF + -939 -939 -939 -939 -939 + -249 -249 -249 -249 -249 + -939 -939 -939 -939 -939 + -329 -329 -329 -329 -329 +/* @.U..UA */ + DEF DEF DEF DEF DEF + -639 -639 -639 -639 -639 + -229 -229 -229 -229 -229 + -729 -729 -729 -729 -729 + -190 -190 -190 -190 -190 +/* @.@.. @ */ + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.A.. @ */ + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.C.. @ */ + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.G.. @ */ + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 +/* @.U.. @ */ + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + -100 -100 -100 -100 -100 + +# int22 +/* CG.AA..CG */ + 130 160 30 200 + 120 150 20 200 + 30 60 -70 200 + 200 200 200 200 +/* CG.AC..CG */ + 160 200 60 200 + 210 180 150 200 + 200 200 200 200 + 190 170 130 200 +/* CG.AG..CG */ + 30 60 -70 200 + 200 200 200 200 + 100 140 0 200 + -40 -110 -60 200 +/* CG.AU..CG */ + 200 200 200 200 + 190 170 130 200 + 110 40 90 200 + 140 80 130 200 +/* CG.CA..CG */ + 120 210 200 190 + 110 140 200 120 + 20 150 200 130 + 200 200 200 200 +/* CG.CC..CG */ + 150 180 200 170 + 140 170 200 150 + 200 200 200 200 + 120 150 200 140 +/* CG.CG..CG */ + 20 150 200 130 + 200 200 200 200 + 90 180 200 170 + -150 -20 200 -40 +/* CG.CU..CG */ + 200 200 200 200 + 120 150 200 140 + 0 130 200 110 + 30 60 200 50 +/* CG.GA..CG */ + 30 200 100 110 + 20 200 90 0 + -70 200 0 90 + 200 200 200 200 +/* CG.GC..CG */ + 60 200 140 40 + 150 200 180 130 + 200 200 200 200 + 130 200 170 110 +/* CG.GG..CG */ + -70 200 0 90 + 200 200 200 200 + 0 200 80 90 + -60 200 -70 -260 +/* CG.GU..CG */ + 200 200 200 200 + 130 200 170 110 + 90 200 90 -110 + 130 200 120 110 +/* CG.UA..CG */ + 200 190 -40 140 + 200 120 -150 30 + 200 130 -60 130 + 200 200 200 200 +/* CG.UC..CG */ + 200 170 -110 80 + 200 150 -20 60 + 200 200 200 200 + 200 140 -40 50 +/* CG.UG..CG */ + 200 130 -60 130 + 200 200 200 200 + 200 170 -70 120 + 200 -40 -420 DEF +/* CG.UU..CG */ + 200 200 200 200 + 200 140 -40 50 + 200 110 -260 110 + 200 50 DEF -40 +/* CG.AA..GC */ + 50 60 0 200 + 110 150 -70 200 + -30 10 -160 200 + 200 200 200 200 +/* CG.AC..GC */ + 110 110 -100 200 + 170 150 -60 200 + 200 200 200 200 + 70 50 20 200 +/* CG.AG..GC */ + 40 50 -70 200 + 200 200 200 200 + 100 140 0 200 + 10 -70 -80 200 +/* CG.AU..GC */ + 200 200 200 200 + 180 150 120 200 + DEF -60 -60 200 + 150 0 90 200 +/* CG.CA..GC */ + 130 220 200 200 + 100 130 200 120 + -70 70 200 40 + 200 200 200 200 +/* CG.CC..GC */ + 100 190 200 110 + 100 130 200 120 + 200 200 200 200 + 0 30 200 170 +/* CG.CG..GC */ + 70 70 200 100 + 200 200 200 200 + 90 180 200 170 + -190 -30 200 -70 +/* CG.CU..GC */ + 200 200 200 200 + 110 140 200 120 + -150 -20 200 -30 + -20 -10 200 20 +/* CG.GA..GC */ + -20 200 110 90 + -40 200 90 0 + -170 200 -90 30 + 200 200 200 200 +/* CG.GC..GC */ + 70 200 80 -10 + 110 200 150 100 + 200 200 200 200 + 20 200 50 0 +/* CG.GG..GC */ + DEF 200 -20 60 + 200 200 200 200 + 0 200 80 90 + -90 200 -100 -300 +/* CG.GU..GC */ + 200 200 200 200 + 120 200 150 100 + -130 200 -60 -240 + 90 200 110 60 +/* CG.UA..GC */ + 200 200 -10 140 + 200 120 -160 30 + 200 40 -160 50 + 200 200 200 200 +/* CG.UC..GC */ + 200 110 -160 30 + 200 120 -60 30 + 200 200 200 200 + 200 20 -160 10 +/* CG.UG..GC */ + 200 50 -60 140 + 200 200 200 200 + 200 170 -70 120 + 200 -70 -440 -100 +/* CG.UU..GC */ + 200 200 200 200 + 200 120 DEF 30 + 200 -10 -410 10 + 200 40 -100 60 +/* CG.AA..GU */ + 200 240 100 200 + 180 210 80 200 + 80 110 -20 200 + 200 200 200 200 +/* CG.AC..GU */ + 190 220 90 200 + 230 210 170 200 + 200 200 200 200 + 230 210 170 200 +/* CG.AG..GU */ + 80 110 -20 200 + 200 200 200 200 + 130 170 30 200 + 60 0 40 200 +/* CG.AU..GU */ + 200 200 200 200 + 230 210 170 200 + 160 90 140 200 + 190 130 180 200 +/* CG.CA..GU */ + 190 280 200 270 + 170 200 200 180 + 70 200 200 180 + 200 200 200 200 +/* CG.CC..GU */ + 180 210 200 190 + 160 190 200 180 + 200 200 200 200 + 160 190 200 180 +/* CG.CG..GU */ + 70 200 200 180 + 200 200 200 200 + 120 210 200 200 + DEF 80 200 70 +/* CG.CU..GU */ + 200 200 200 200 + 160 190 200 180 + 50 180 200 160 + 80 110 200 100 +/* CG.GA..GU */ + 100 200 180 180 + 80 200 150 60 + -20 200 50 140 + 200 200 200 200 +/* CG.GC..GU */ + 90 200 160 70 + 170 200 210 150 + 200 200 200 200 + 170 200 210 150 +/* CG.GG..GU */ + -20 200 50 140 + 200 200 200 200 + 30 200 110 110 + 40 200 40 -160 +/* CG.GU..GU */ + 200 200 200 200 + 170 200 210 150 + 140 200 130 -60 + 180 200 170 160 +/* CG.UA..GU */ + 200 270 30 220 + 200 180 -90 90 + 200 180 -10 180 + 200 200 200 200 +/* CG.UC..GU */ + 200 190 -80 100 + 200 180 0 90 + 200 200 200 200 + 200 180 0 90 +/* CG.UG..GU */ + 200 180 -10 180 + 200 200 200 200 + 200 200 -40 150 + 200 70 -310 60 +/* CG.UU..GU */ + 200 200 200 200 + 200 180 0 90 + 200 160 -210 160 + 200 100 0 10 +/* CG.AA..UG */ + 200 240 100 200 + 160 190 60 200 + 100 130 0 200 + 200 200 200 200 +/* CG.AC..UG */ + 200 240 100 200 + 260 240 200 200 + 200 200 200 200 + 260 240 200 200 +/* CG.AG..UG */ + 100 130 0 200 + 200 200 200 200 + 140 170 40 200 + 20 -40 0 200 +/* CG.AU..UG */ + 200 200 200 200 + 230 210 170 200 + 150 80 130 200 + 220 150 200 200 +/* CG.CA..UG */ + 190 280 200 270 + 150 180 200 160 + 90 220 200 200 + 200 200 200 200 +/* CG.CC..UG */ + 190 220 200 210 + 190 220 200 210 + 200 200 200 200 + 190 220 200 210 +/* CG.CG..UG */ + 90 220 200 200 + 200 200 200 200 + 130 220 200 200 + -90 40 200 30 +/* CG.CU..UG */ + 200 200 200 200 + 160 190 200 180 + 40 170 200 150 + 110 140 200 120 +/* CG.GA..UG */ + 100 200 180 180 + 60 200 130 40 + 0 200 70 160 + 200 200 200 200 +/* CG.GC..UG */ + 100 200 180 80 + 200 200 240 180 + 200 200 200 200 + 200 200 240 180 +/* CG.GG..UG */ + 0 200 70 160 + 200 200 200 200 + 40 200 110 120 + 0 200 0 -200 +/* CG.GU..UG */ + 200 200 200 200 + 170 200 210 150 + 130 200 120 -70 + 200 200 190 180 +/* CG.UA..UG */ + 200 270 30 220 + 200 160 -110 70 + 200 200 10 190 + 200 200 200 200 +/* CG.UC..UG */ + 200 210 -70 120 + 200 210 30 120 + 200 200 200 200 + 200 210 30 120 +/* CG.UG..UG */ + 200 200 10 190 + 200 200 200 200 + 200 200 -30 150 + 200 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GC.UU..GC */ + -1378 -1378 -1378 -1448 + -888 -888 -888 -958 + -1238 -1238 -1238 -1308 + -1068 -1068 -1068 -1138 +/* GC.AA..GU */ + -948 -1308 -988 -1308 + -778 -1138 -818 -1138 + -858 -1218 -898 -1218 + -848 -1208 -888 -1208 +/* GC.AC..GU */ + -1118 -1478 -1158 -1478 + -758 -1118 -798 -1118 + -1208 -1568 -1248 -1568 + -848 -1208 -888 -1208 +/* GC.AG..GU */ + -1118 -1478 -1158 -1478 + -758 -1118 -798 -1118 + -1208 -1568 -1248 -1568 + -848 -1208 -888 -1208 +/* GC.AU..GU */ + -1118 -1478 -1158 -1478 + -758 -1118 -798 -1118 + -1208 -1568 -1248 -1568 + -848 -1208 -888 -1208 +/* GC.CA..GU */ + -1148 -738 -738 -818 + -978 -568 -568 -648 + -1058 -648 -648 -728 + -1048 -638 -638 -718 +/* GC.CC..GU */ + -1318 -908 -908 -988 + -958 -548 -548 -628 + -1408 -998 -998 -1078 + -1048 -638 -638 -718 +/* GC.CG..GU */ + -1318 -908 -908 -988 + -958 -548 -548 -628 + -1408 -998 -998 -1078 + -1048 -638 -638 -718 +/* GC.CU..GU */ + -1318 -908 -908 -988 + -958 -548 -548 -628 + -1408 -998 -998 -1078 + -1048 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-1498 -1528 -1408 -1528 + -1188 -1218 -1098 -1218 + -1518 -1548 -1428 -1548 + -1148 -1178 -1058 -1178 +/* GC.GG..UG */ + -1668 -1698 -1578 -1698 + -1068 -1098 -978 -1098 + -1628 -1658 -1538 -1658 + -1258 -1288 -1168 -1288 +/* GC.GU..UG */ + -1518 -1548 -1428 -1548 + -1188 -1218 -1098 -1218 + -1518 -1548 -1428 -1548 + -1068 -1098 -978 -1098 +/* GC.UA..UG */ + -1218 -1218 -1218 -1288 + -978 -978 -978 -1048 + -1158 -1158 -1158 -1228 + -1048 -1048 -1048 -1118 +/* GC.UC..UG */ + -1288 -1288 -1288 -1358 + -978 -978 -978 -1048 + -1308 -1308 -1308 -1378 + -938 -938 -938 -1008 +/* GC.UG..UG */ + -1458 -1458 -1458 -1528 + -858 -858 -858 -928 + -1418 -1418 -1418 -1488 + -1048 -1048 -1048 -1118 +/* GC.UU..UG */ + -1308 -1308 -1308 -1378 + -978 -978 -978 -1048 + -1308 -1308 -1308 -1378 + -858 -858 -858 -928 +/* GC.AA..AU */ + -948 -1308 -988 -1308 + -778 -1138 -818 -1138 + -858 -1218 -898 -1218 + -848 -1208 -888 -1208 +/* GC.AC..AU */ + -1118 -1478 -1158 -1478 + -758 -1118 -798 -1118 + -1208 -1568 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-898 -898 -898 -968 + -928 -928 -928 -998 + -878 -878 -878 -948 + -778 -778 -778 -848 +/* GC.UC..UA */ + -1128 -1128 -1128 -1198 + -1008 -1008 -1008 -1078 + -1178 -1178 -1178 -1248 + -638 -638 -638 -708 +/* GC.UG..UA */ + -1388 -1388 -1388 -1458 + -698 -698 -698 -768 + -1388 -1388 -1388 -1458 + -778 -778 -778 -848 +/* GC.UU..UA */ + -1088 -1088 -1088 -1158 + -678 -678 -678 -748 + -1178 -1178 -1178 -1248 + -639 -639 -639 -709 +/* GU.AA..CG */ + -1458 -1628 -1628 -1628 + -948 -1118 -1118 -1118 + -1368 -1538 -1538 -1538 + -1238 -1408 -1408 -1408 +/* GU.AC..CG */ + -1378 -1548 -1548 -1548 + -878 -1048 -1048 -1048 + -1368 -1538 -1538 -1538 + -1168 -1338 -1338 -1338 +/* GU.AG..CG */ + -1458 -1628 -1628 -1628 + -948 -1118 -1118 -1118 + -1368 -1538 -1538 -1538 + -1238 -1408 -1408 -1408 +/* GU.AU..CG */ + -1458 -1628 -1628 -1628 + -1098 -1268 -1268 -1268 + -1368 -1538 -1538 -1538 + -1288 -1458 -1458 -1458 +/* GU.CA..CG */ + -1288 -1268 -1268 -1268 + -778 -758 -758 -758 + -1198 -1178 -1178 -1178 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UG.CU..GC */ + -1358 -1358 -1238 -1358 + -868 -868 -748 -868 + -1218 -1218 -1098 -1218 + -1048 -1048 -928 -1048 +/* UG.GA..GC */ + -1178 -1328 -1438 -1328 + -1378 -1528 -1638 -1528 + -1368 -1518 -1628 -1518 + -1158 -1308 -1418 -1308 +/* UG.GC..GC */ + -1538 -1688 -1798 -1688 + -968 -1118 -1228 -1118 + -1398 -1548 -1658 -1548 + -1158 -1308 -1418 -1308 +/* UG.GG..GC */ + -1218 -1368 -1478 -1368 + -968 -1118 -1228 -1118 + -1278 -1428 -1538 -1428 + -1158 -1308 -1418 -1308 +/* UG.GU..GC */ + -1538 -1688 -1798 -1688 + -1048 -1198 -1308 -1198 + -1398 -1548 -1658 -1548 + -1228 -1378 -1488 -1378 +/* UG.UA..GC */ + -1068 -958 -1068 -878 + -1268 -1158 -1268 -1078 + -1258 -1148 -1258 -1068 + -1048 -938 -1048 -858 +/* UG.UC..GC */ + -1428 -1318 -1428 -1238 + -858 -748 -858 -668 + -1288 -1178 -1288 -1098 + -1048 -938 -1048 -858 +/* UG.UG..GC */ + -1108 -998 -1108 -918 + -858 -748 -858 -668 + -1168 -1058 -1168 -978 + -1048 -938 -1048 -858 +/* UG.UU..GC */ + -1428 -1318 -1428 -1238 + -938 -828 -938 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*/ + -1308 -1378 -1548 -1398 + -898 -968 -1138 -988 + -1398 -1468 -1638 -1488 + -859 -929 -1099 -949 +/* UG.CA..UA */ + -878 -878 -758 -878 + -908 -908 -788 -908 + -858 -858 -738 -858 + -758 -758 -638 -758 +/* UG.CC..UA */ + -1108 -1108 -988 -1108 + -988 -988 -868 -988 + -1158 -1158 -1038 -1158 + -618 -618 -498 -618 +/* UG.CG..UA */ + -1368 -1368 -1248 -1368 + -678 -678 -558 -678 + -1368 -1368 -1248 -1368 + -758 -758 -638 -758 +/* UG.CU..UA */ + -1068 -1068 -948 -1068 + -658 -658 -538 -658 + -1158 -1158 -1038 -1158 + -619 -619 -499 -619 +/* UG.GA..UA */ + -1058 -1208 -1318 -1208 + -1088 -1238 -1348 -1238 + -1038 -1188 -1298 -1188 + -938 -1088 -1198 -1088 +/* UG.GC..UA */ + -1288 -1438 -1548 -1438 + -1168 -1318 -1428 -1318 + -1338 -1488 -1598 -1488 + -798 -948 -1058 -948 +/* UG.GG..UA */ + -1548 -1698 -1808 -1698 + -858 -1008 -1118 -1008 + -1548 -1698 -1808 -1698 + -938 -1088 -1198 -1088 +/* UG.GU..UA */ + -1248 -1398 -1508 -1398 + -838 -988 -1098 -988 + -1338 -1488 -1598 -1488 + -799 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-838 -838 -838 + -1008 -1008 -1008 -1008 + -468 -468 -468 -468 +/* AU.UG..UA */ + -1218 -1218 -1218 -1218 + -528 -528 -528 -528 + -1218 -1218 -1218 -1218 + -608 -608 -608 -608 +/* AU.UU..UA */ + -918 -918 -918 -918 + -508 -508 -508 -508 + -1008 -1008 -1008 -1008 + -469 -469 -469 -469 +/* UA.AA..CG */ + -1428 -1658 -1918 -1618 + -918 -1148 -1408 -1108 + -1338 -1568 -1828 -1528 + -1208 -1438 -1698 -1398 +/* UA.AC..CG */ + -1348 -1578 -1838 -1538 + -848 -1078 -1338 -1038 + -1338 -1568 -1828 -1528 + -1138 -1368 -1628 -1328 +/* UA.AG..CG */ + -1428 -1658 -1918 -1618 + -918 -1148 -1408 -1108 + -1338 -1568 -1828 -1528 + -1208 -1438 -1698 -1398 +/* UA.AU..CG */ + -1428 -1658 -1918 -1618 + -1068 -1298 -1558 -1258 + -1338 -1568 -1828 -1528 + -1258 -1488 -1748 -1448 +/* UA.CA..CG */ + -1458 -1538 -1228 -1208 + -948 -1028 -718 -698 + -1368 -1448 -1138 -1118 + -1238 -1318 -1008 -988 +/* UA.CC..CG */ + -1378 -1458 -1148 -1128 + -878 -958 -648 -628 + -1368 -1448 -1138 -1118 + -1168 -1248 -938 -918 +/* UA.CG..CG */ + -1458 -1538 -1228 -1208 + -948 -1028 -718 -698 + -1368 -1448 -1138 -1118 + -1238 -1318 -1008 -988 +/* UA.CU..CG */ + -1458 -1538 -1228 -1208 + -1098 -1178 -868 -848 + -1368 -1448 -1138 -1118 + -1288 -1368 -1058 -1038 +/* UA.GA..CG */ + -1408 -1708 -1918 -1708 + -898 -1198 -1408 -1198 + -1318 -1618 -1828 -1618 + -1188 -1488 -1698 -1488 +/* UA.GC..CG */ + -1328 -1628 -1838 -1628 + -828 -1128 -1338 -1128 + -1318 -1618 -1828 -1618 + -1118 -1418 -1628 -1418 +/* UA.GG..CG */ + -1408 -1708 -1918 -1708 + -898 -1198 -1408 -1198 + -1318 -1618 -1828 -1618 + -1188 -1488 -1698 -1488 +/* UA.GU..CG */ + -1408 -1708 -1918 -1708 + -1048 -1348 -1558 -1348 + -1318 -1618 -1828 -1618 + -1238 -1538 -1748 -1538 +/* UA.UA..CG */ + -1308 -1168 -1308 -1169 + -798 -658 -798 -659 + -1218 -1078 -1218 -1079 + -1088 -948 -1088 -949 +/* UA.UC..CG */ + -1228 -1088 -1228 -1089 + -728 -588 -728 -589 + -1218 -1078 -1218 -1079 + -1018 -878 -1018 -879 +/* UA.UG..CG */ + -1308 -1168 -1308 -1169 + -798 -658 -798 -659 + -1218 -1078 -1218 -1079 + -1088 -948 -1088 -949 +/* UA.UU..CG */ + -1308 -1168 -1308 -1169 + -948 -808 -948 -809 + -1218 -1078 -1218 -1079 + -1138 -998 -1138 -999 +/* UA.AA..GC */ + -918 -1148 -1408 -1108 + -1118 -1348 -1608 -1308 + -1108 -1338 -1598 -1298 + -898 -1128 -1388 -1088 +/* UA.AC..GC */ + -1278 -1508 -1768 -1468 + -708 -938 -1198 -898 + -1138 -1368 -1628 -1328 + -898 -1128 -1388 -1088 +/* UA.AG..GC */ + -958 -1188 -1448 -1148 + -708 -938 -1198 -898 + -1018 -1248 -1508 -1208 + -898 -1128 -1388 -1088 +/* UA.AU..GC */ + -1278 -1508 -1768 -1468 + -788 -1018 -1278 -978 + -1138 -1368 -1628 -1328 + -968 -1198 -1458 -1158 +/* UA.CA..GC */ + -948 -1028 -718 -698 + -1148 -1228 -918 -898 + -1138 -1218 -908 -888 + -928 -1008 -698 -678 +/* UA.CC..GC */ + -1308 -1388 -1078 -1058 + -738 -818 -508 -488 + -1168 -1248 -938 -918 + -928 -1008 -698 -678 +/* UA.CG..GC */ + -988 -1068 -758 -738 + -738 -818 -508 -488 + -1048 -1128 -818 -798 + -928 -1008 -698 -678 +/* UA.CU..GC */ + -1308 -1388 -1078 -1058 + -818 -898 -588 -568 + -1168 -1248 -938 -918 + -998 -1078 -768 -748 +/* UA.GA..GC */ + -898 -1198 -1408 -1198 + -1098 -1398 -1608 -1398 + -1088 -1388 -1598 -1388 + -878 -1178 -1388 -1178 +/* UA.GC..GC */ + -1258 -1558 -1768 -1558 + -688 -988 -1198 -988 + -1118 -1418 -1628 -1418 + -878 -1178 -1388 -1178 +/* UA.GG..GC */ + -938 -1238 -1448 -1238 + -688 -988 -1198 -988 + -998 -1298 -1508 -1298 + -878 -1178 -1388 -1178 +/* UA.GU..GC */ + -1258 -1558 -1768 -1558 + -768 -1068 -1278 -1068 + -1118 -1418 -1628 -1418 + -948 -1248 -1458 -1248 +/* UA.UA..GC */ + -798 -658 -798 -659 + -998 -858 -998 -859 + -988 -848 -988 -849 + -778 -638 -778 -639 +/* UA.UC..GC */ + -1158 -1018 -1158 -1019 + -588 -448 -588 -449 + -1018 -878 -1018 -879 + -778 -638 -778 -639 +/* UA.UG..GC */ + -838 -698 -838 -699 + -588 -448 -588 -449 + -898 -758 -898 -759 + -778 -638 -778 -639 +/* UA.UU..GC */ + -1158 -1018 -1158 -1019 + -668 -528 -668 -529 + -1018 -878 -1018 -879 + -848 -708 -848 -709 +/* UA.AA..GU */ + -828 -1058 -1318 -1018 + -658 -888 -1148 -848 + -738 -968 -1228 -928 + -728 -958 -1218 -918 +/* UA.AC..GU */ + -998 -1228 -1488 -1188 + -638 -868 -1128 -828 + -1088 -1318 -1578 -1278 + -728 -958 -1218 -918 +/* UA.AG..GU */ + -998 -1228 -1488 -1188 + -638 -868 -1128 -828 + -1088 -1318 -1578 -1278 + -728 -958 -1218 -918 +/* UA.AU..GU */ + -998 -1228 -1488 -1188 + -638 -868 -1128 -828 + -1088 -1318 -1578 -1278 + -728 -958 -1218 -918 +/* UA.CA..GU */ + -858 -938 -628 -608 + -688 -768 -458 -438 + -768 -848 -538 -518 + -758 -838 -528 -508 +/* UA.CC..GU */ + -1028 -1108 -798 -778 + -668 -748 -438 -418 + -1118 -1198 -888 -868 + -758 -838 -528 -508 +/* UA.CG..GU */ + -1028 -1108 -798 -778 + -668 -748 -438 -418 + -1118 -1198 -888 -868 + -758 -838 -528 -508 +/* UA.CU..GU */ + -1028 -1108 -798 -778 + -668 -748 -438 -418 + -1118 -1198 -888 -868 + -758 -838 -528 -508 +/* UA.GA..GU */ + -808 -1108 -1318 -1108 + -638 -938 -1148 -938 + -718 -1018 -1228 -1018 + -708 -1008 -1218 -1008 +/* UA.GC..GU */ + -978 -1278 -1488 -1278 + -618 -918 -1128 -918 + -1068 -1368 -1578 -1368 + -708 -1008 -1218 -1008 +/* UA.GG..GU */ + -978 -1278 -1488 -1278 + -618 -918 -1128 -918 + -1068 -1368 -1578 -1368 + -708 -1008 -1218 -1008 +/* UA.GU..GU */ + -978 -1278 -1488 -1278 + -618 -918 -1128 -918 + -1068 -1368 -1578 -1368 + -708 -1008 -1218 -1008 +/* UA.UA..GU */ + -708 -568 -708 -569 + -538 -398 -538 -399 + -618 -478 -618 -479 + -608 -468 -608 -469 +/* UA.UC..GU */ + -878 -738 -878 -739 + -518 -378 -518 -379 + -968 -828 -968 -829 + -608 -468 -608 -469 +/* UA.UG..GU */ + -878 -738 -878 -739 + -518 -378 -518 -379 + -968 -828 -968 -829 + -608 -468 -608 -469 +/* UA.UU..GU */ + -878 -738 -878 -739 + -518 -378 -518 -379 + -968 -828 -968 -829 + -608 -468 -608 -469 +/* UA.AA..UG */ + -1118 -1348 -1608 -1308 + -878 -1108 -1368 -1068 + -1058 -1288 -1548 -1248 + -948 -1178 -1438 -1138 +/* UA.AC..UG */ + -1188 -1418 -1678 -1378 + -878 -1108 -1368 -1068 + -1208 -1438 -1698 -1398 + -838 -1068 -1328 -1028 +/* UA.AG..UG */ + -1358 -1588 -1848 -1548 + -758 -988 -1248 -948 + -1318 -1548 -1808 -1508 + -948 -1178 -1438 -1138 +/* UA.AU..UG */ + -1208 -1438 -1698 -1398 + -878 -1108 -1368 -1068 + -1208 -1438 -1698 -1398 + -758 -988 -1248 -948 +/* UA.CA..UG */ + -1148 -1228 -918 -898 + -908 -988 -678 -658 + -1088 -1168 -858 -838 + -978 -1058 -748 -728 +/* UA.CC..UG */ + -1218 -1298 -988 -968 + -908 -988 -678 -658 + -1238 -1318 -1008 -988 + -868 -948 -638 -618 +/* UA.CG..UG */ + -1388 -1468 -1158 -1138 + -788 -868 -558 -538 + -1348 -1428 -1118 -1098 + -978 -1058 -748 -728 +/* UA.CU..UG */ + -1238 -1318 -1008 -988 + -908 -988 -678 -658 + -1238 -1318 -1008 -988 + -788 -868 -558 -538 +/* UA.GA..UG */ + -1098 -1398 -1608 -1398 + -858 -1158 -1368 -1158 + -1038 -1338 -1548 -1338 + -928 -1228 -1438 -1228 +/* UA.GC..UG */ + -1168 -1468 -1678 -1468 + -858 -1158 -1368 -1158 + -1188 -1488 -1698 -1488 + -818 -1118 -1328 -1118 +/* UA.GG..UG */ + -1338 -1638 -1848 -1638 + -738 -1038 -1248 -1038 + -1298 -1598 -1808 -1598 + -928 -1228 -1438 -1228 +/* UA.GU..UG */ + -1188 -1488 -1698 -1488 + -858 -1158 -1368 -1158 + -1188 -1488 -1698 -1488 + -738 -1038 -1248 -1038 +/* UA.UA..UG */ + -998 -858 -998 -859 + -758 -618 -758 -619 + -938 -798 -938 -799 + -828 -688 -828 -689 +/* UA.UC..UG */ + -1068 -928 -1068 -929 + -758 -618 -758 -619 + -1088 -948 -1088 -949 + -718 -578 -718 -579 +/* UA.UG..UG */ + -1238 -1098 -1238 -1099 + -638 -498 -638 -499 + -1198 -1058 -1198 -1059 + -828 -688 -828 -689 +/* UA.UU..UG */ + -1088 -948 -1088 -949 + -758 -618 -758 -619 + -1088 -948 -1088 -949 + -638 -498 -638 -499 +/* UA.AA..AU */ + -828 -1058 -1318 -1018 + -658 -888 -1148 -848 + -738 -968 -1228 -928 + -728 -958 -1218 -918 +/* UA.AC..AU */ + -998 -1228 -1488 -1188 + -638 -868 -1128 -828 + -1088 -1318 -1578 -1278 + -728 -958 -1218 -918 +/* UA.AG..AU */ + -998 -1228 -1488 -1188 + -638 -868 -1128 -828 + -1088 -1318 -1578 -1278 + -728 -958 -1218 -918 +/* UA.AU..AU */ + -998 -1228 -1488 -1188 + -638 -868 -1128 -828 + -1088 -1318 -1578 -1278 + -728 -958 -1218 -918 +/* UA.CA..AU */ + -858 -938 -628 -608 + -688 -768 -458 -438 + -768 -848 -538 -518 + -758 -838 -528 -508 +/* UA.CC..AU */ + -1028 -1108 -798 -778 + -668 -748 -438 -418 + -1118 -1198 -888 -868 + -758 -838 -528 -508 +/* UA.CG..AU */ + -1028 -1108 -798 -778 + -668 -748 -438 -418 + -1118 -1198 -888 -868 + -758 -838 -528 -508 +/* UA.CU..AU */ + -1028 -1108 -798 -778 + -668 -748 -438 -418 + -1118 -1198 -888 -868 + -758 -838 -528 -508 +/* UA.GA..AU */ + -808 -1108 -1318 -1108 + -638 -938 -1148 -938 + -718 -1018 -1228 -1018 + -708 -1008 -1218 -1008 +/* UA.GC..AU */ + -978 -1278 -1488 -1278 + -618 -918 -1128 -918 + -1068 -1368 -1578 -1368 + -708 -1008 -1218 -1008 +/* UA.GG..AU */ + -978 -1278 -1488 -1278 + -618 -918 -1128 -918 + -1068 -1368 -1578 -1368 + -708 -1008 -1218 -1008 +/* UA.GU..AU */ + -978 -1278 -1488 -1278 + -618 -918 -1128 -918 + -1068 -1368 -1578 -1368 + -708 -1008 -1218 -1008 +/* UA.UA..AU */ + -708 -568 -708 -569 + -538 -398 -538 -399 + -618 -478 -618 -479 + -608 -468 -608 -469 +/* UA.UC..AU */ + -878 -738 -878 -739 + -518 -378 -518 -379 + -968 -828 -968 -829 + -608 -468 -608 -469 +/* UA.UG..AU */ + -878 -738 -878 -739 + -518 -378 -518 -379 + -968 -828 -968 -829 + -608 -468 -608 -469 +/* UA.UU..AU */ + -878 -738 -878 -739 + -518 -378 -518 -379 + -968 -828 -968 -829 + -608 -468 -608 -469 +/* UA.AA..UA */ + -798 -1028 -1288 -988 + -828 -1058 -1318 -1018 + -778 -1008 -1268 -968 + -678 -908 -1168 -868 +/* UA.AC..UA */ + -1028 -1258 -1518 -1218 + -908 -1138 -1398 -1098 + -1078 -1308 -1568 -1268 + -538 -768 -1028 -728 +/* UA.AG..UA */ + -1288 -1518 -1778 -1478 + -598 -828 -1088 -788 + -1288 -1518 -1778 -1478 + -678 -908 -1168 -868 +/* UA.AU..UA */ + -988 -1218 -1478 -1178 + -578 -808 -1068 -768 + -1078 -1308 -1568 -1268 + -539 -769 -1029 -729 +/* UA.CA..UA */ + -828 -908 -598 -578 + -858 -938 -628 -608 + -808 -888 -578 -558 + -708 -788 -478 -458 +/* UA.CC..UA */ + -1058 -1138 -828 -808 + -938 -1018 -708 -688 + -1108 -1188 -878 -858 + -568 -648 -338 -318 +/* UA.CG..UA */ + -1318 -1398 -1088 -1068 + -628 -708 -398 -378 + -1318 -1398 -1088 -1068 + -708 -788 -478 -458 +/* UA.CU..UA */ + -1018 -1098 -788 -768 + -608 -688 -378 -358 + -1108 -1188 -878 -858 + -569 -649 -339 -319 +/* UA.GA..UA */ + -778 -1078 -1288 -1078 + -808 -1108 -1318 -1108 + -758 -1058 -1268 -1058 + -658 -958 -1168 -958 +/* UA.GC..UA */ + -1008 -1308 -1518 -1308 + -888 -1188 -1398 -1188 + -1058 -1358 -1568 -1358 + -518 -818 -1028 -818 +/* UA.GG..UA */ + -1268 -1568 -1778 -1568 + -578 -878 -1088 -878 + -1268 -1568 -1778 -1568 + -658 -958 -1168 -958 +/* UA.GU..UA */ + -968 -1268 -1478 -1268 + -558 -858 -1068 -858 + -1058 -1358 -1568 -1358 + -519 -819 -1029 -819 +/* UA.UA..UA */ + -678 -538 -678 -539 + -708 -568 -708 -569 + -658 -518 -658 -519 + -558 -418 -558 -419 +/* UA.UC..UA */ + -908 -768 -908 -769 + -788 -648 -788 -649 + -958 -818 -958 -819 + -418 -278 -418 -279 +/* UA.UG..UA */ + -1168 -1028 -1168 -1029 + -478 -338 -478 -339 + -1168 -1028 -1168 -1029 + -558 -418 -558 -419 +/* UA.UU..UA */ + -868 -728 -868 -729 + -458 -318 -458 -319 + -958 -818 -958 -819 + -419 -279 -419 -280 + +# hairpin + INF INF INF 570 560 560 540 590 560 640 + 650 660 670 678 686 694 701 707 713 719 + 725 730 735 740 744 749 753 757 761 765 + 769 + +# hairpin_enthalpies + INF INF INF 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 + 0 + +# bulge + INF 380 280 320 360 400 440 459 470 480 + 490 500 510 519 527 534 541 548 554 560 + 565 571 576 580 585 589 594 598 602 605 + 609 + +# bulge_enthalpies + INF 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 + 0 + +# interior + INF INF 410 510 170 180 200 220 230 240 + 250 260 270 278 286 294 301 307 313 319 + 325 330 335 340 345 349 353 357 361 365 + 369 + +# interior_enthalpies + INF INF INF INF 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 + 0 + +# NINIO +/* Ninio = MIN(max, m*|n1-n2| */ +/* m m_dH max */ + 50 0 300 + +# ML_params +/* F = cu*n_unpaired + cc + ci*loop_degree (+TermAU) */ +/* cu cu_dH cc cc_dH ci ci_dH */ + 0 0 340 0 40 0 + +# Misc +/* all parameters are pairs of 'energy enthalpy' */ +/* DuplexInit TerminalAU LXC */ + 410 0 50 0 107.856000 0 + +# Triloops + +# Tetraloops + GGGGAC 20 -1110 + GGUGAC 20 -1110 + CGAAAG 40 -1340 + GGAGAC 20 -1110 + CGCAAG 40 -1340 + GGAAAC 20 -1110 + CGGAAG 40 -1340 + CUUCGG 80 -1210 + CGUGAG 40 -1340 + CGAAGG 150 -1340 + CUACGG 130 -1210 + GGCAAC 70 -1110 + CGCGAG 90 -1340 + UGAGAG 230 -1060 + CGAGAG 140 -1340 + AGAAAU 250 -740 + CGUAAG 140 -1340 + CUAACG 220 -1140 + UGAAAG 280 -1060 + GGAAGC 270 -1020 + GGGAAC 170 -1110 + UGAAAA 270 -780 + AGCAAU 300 -740 + AGUAAU 300 -740 + CGGGAG 190 -1340 + AGUGAU 300 -740 + GGCGAC 170 -1110 + GGGAGC 270 -1020 + GUGAAC 220 -900 + UGGAAA 270 -780 + +# Hexaloops + + +# END diff --git a/src/energy_params/rna_turner2004.par b/src/energy_params/rna_turner2004.par new file mode 100644 index 0000000..4fb06e1 --- /dev/null +++ b/src/energy_params/rna_turner2004.par @@ -0,0 +1,8142 @@ +## RNAfold parameter file v2.0 + +# stack +/* CG GC GU UG AU UA NN */ + -240 -330 -210 -140 -210 -210 -140 /* CG */ + -330 -340 -250 -150 -220 -240 -150 /* GC */ + -210 -250 130 -50 -140 -130 130 /* GU */ + -140 -150 -50 30 -60 -100 30 /* UG */ + -210 -220 -140 -60 -110 -90 -60 /* AU */ + -210 -240 -130 -100 -90 -130 -90 /* UA */ + -140 -150 130 30 -60 -90 130 /* NN */ + +# stack_enthalpies +/* CG GC GU UG AU UA NN */ + -1060 -1340 -1210 -560 -1050 -1040 -560 /* CG */ + -1340 -1490 -1260 -830 -1140 -1240 -830 /* GC */ + -1210 -1260 -1460 -1350 -880 -1280 -880 /* GU */ + -560 -830 -1350 -930 -320 -700 -320 /* UG */ + -1050 -1140 -880 -320 -940 -680 -320 /* AU */ + -1040 -1240 -1280 -700 -680 -770 -680 /* UA */ + -560 -830 -880 -320 -320 -680 -320 /* NN */ + +# mismatch_hairpin + -80 -100 -110 -100 -80 /* CG,E */ + -140 -150 -150 -140 -150 /* CG,A */ + -80 -100 -110 -100 -80 /* CG,C */ + -150 -230 -150 -240 -150 /* CG,G */ + -100 -100 -140 -100 -210 /* CG,U */ + -50 -110 -70 -110 -50 /* GC,E */ + -110 -110 -150 -130 -150 /* GC,A */ + -50 -110 -70 -110 -50 /* GC,C */ + -150 -250 -150 -220 -150 /* GC,G */ + -100 -110 -100 -110 -160 /* GC,U */ + 20 20 -20 -10 -20 /* GU,E */ + 20 20 -50 -30 -50 /* GU,A */ + -10 -10 -20 -10 -20 /* GU,C */ + -50 -100 -50 -110 -50 /* GU,G */ + -10 -10 -30 -10 -100 /* GU,U */ + 0 -20 -10 -20 0 /* UG,E */ + -30 -50 -30 -60 -30 /* UG,A */ + 0 -20 -10 -20 0 /* UG,C */ + -30 -90 -30 -110 -30 /* UG,G */ + -10 -20 -10 -20 -90 /* UG,U */ + -10 -10 -20 -10 -20 /* AU,E */ + -30 -30 -50 -30 -50 /* AU,A */ + -10 -10 -20 -10 -20 /* AU,C */ + -50 -120 -50 -110 -50 /* AU,G */ + -10 -10 -30 -10 -120 /* AU,U */ + 0 -20 -10 -20 0 /* UA,E */ + -30 -50 -30 -50 -30 /* UA,A */ + 0 -20 -10 -20 0 /* UA,C */ + -30 -150 -30 -150 -30 /* UA,G */ + -10 -20 -10 -20 -90 /* UA,U */ + 20 20 -10 -10 0 /* NS,E */ + 20 20 -30 -30 -30 /* NS,A */ + 0 -10 -10 -10 0 /* NS,C */ + -30 -90 -30 -110 -30 /* NS,G */ + -10 -10 -10 -10 -90 /* NS,U */ + +# mismatch_hairpin_enthalpies + 560 -570 560 -560 -270 /* CG,E */ + -560 -910 -560 -560 -560 /* CG,A */ + -270 -570 -340 -570 -270 /* CG,C */ + 560 -1400 560 -920 -560 /* CG,G */ + -530 -570 -530 -570 -1440 /* CG,U */ + 50 -520 50 -560 -400 /* GC,E */ + -400 -520 -400 -560 -400 /* GC,A */ + 50 -720 50 -720 -420 /* GC,C */ + -400 -1290 -400 -620 -400 /* GC,G */ + -30 -720 -30 -720 -1080 /* GC,U */ + 970 140 970 140 570 /* GU,E */ + 570 30 570 20 570 /* GU,A */ + 970 140 970 140 340 /* GU,C */ + 570 -270 570 20 570 /* GU,G */ + 830 140 830 140 -50 /* GU,U */ + 230 100 230 220 190 /* UG,E */ + -110 -110 -260 -520 -260 /* UG,A */ + 190 -60 -140 -60 190 /* UG,C */ + 220 100 -260 220 -260 /* UG,G */ + 230 -60 230 -60 -70 /* UG,U */ + 970 140 970 140 570 /* AU,E */ + 570 -20 570 20 570 /* AU,A */ + 970 140 970 140 340 /* AU,C */ + 570 -520 570 20 570 /* AU,G */ + 830 140 830 140 -380 /* AU,U */ + 230 -30 230 -60 190 /* UA,E */ + -30 -30 -260 -520 -260 /* UA,A */ + 190 -60 -140 -60 190 /* UA,C */ + -260 -590 -260 -520 -260 /* UA,G */ + 230 -60 230 -60 -70 /* UA,U */ + 970 140 970 220 570 /* NS,E */ + 570 30 570 20 570 /* NS,A */ + 970 140 970 140 340 /* NS,C */ + 570 100 570 220 570 /* NS,G */ + 830 140 830 140 -50 /* NS,U */ + +# mismatch_interior + 0 0 0 0 0 /* CG,E */ + 0 0 0 -80 0 /* CG,A */ + 0 0 0 0 0 /* CG,C */ + 0 -100 0 -100 0 /* CG,G */ + 0 0 0 0 -60 /* CG,U */ + 0 0 0 0 0 /* GC,E */ + 0 0 0 -80 0 /* GC,A */ + 0 0 0 0 0 /* GC,C */ + 0 -100 0 -100 0 /* GC,G */ + 0 0 0 0 -60 /* GC,U */ + 70 70 70 70 70 /* GU,E */ + 70 70 70 -10 70 /* GU,A */ + 70 70 70 70 70 /* GU,C */ + 70 -30 70 -30 70 /* GU,G */ + 70 70 70 70 10 /* GU,U */ + 70 70 70 70 70 /* UG,E */ + 70 70 70 -10 70 /* UG,A */ + 70 70 70 70 70 /* UG,C */ + 70 -30 70 -30 70 /* UG,G */ + 70 70 70 70 10 /* UG,U */ + 70 70 70 70 70 /* AU,E */ + 70 70 70 -10 70 /* AU,A */ + 70 70 70 70 70 /* AU,C */ + 70 -30 70 -30 70 /* AU,G */ + 70 70 70 70 10 /* AU,U */ + 70 70 70 70 70 /* UA,E */ + 70 70 70 -10 70 /* UA,A */ + 70 70 70 70 70 /* UA,C */ + 70 -30 70 -30 70 /* UA,G */ + 70 70 70 70 10 /* UA,U */ + 70 70 70 70 70 /* NS,E */ + 70 70 70 -10 70 /* NS,A */ + 70 70 70 70 70 /* NS,C */ + 70 -30 70 -30 70 /* NS,G */ + 70 70 70 70 10 /* NS,U */ + +# mismatch_interior_enthalpies + 280 0 0 280 0 /* CG,E */ + 0 0 0 -340 0 /* CG,A */ + 0 0 0 0 0 /* CG,C */ + 280 -760 0 280 0 /* CG,G */ + 0 0 0 0 -580 /* CG,U */ + 280 0 0 280 0 /* GC,E */ + 0 0 0 -340 0 /* GC,A */ + 0 0 0 0 0 /* GC,C */ + 280 -760 0 280 0 /* GC,G */ + 0 0 0 0 -580 /* GC,U */ + 790 500 500 790 500 /* GU,E */ + 500 500 500 170 500 /* GU,A */ + 500 500 500 500 500 /* GU,C */ + 790 -260 500 790 500 /* GU,G */ + 500 500 500 500 -80 /* GU,U */ + 790 500 500 790 500 /* UG,E */ + 500 500 500 170 500 /* UG,A */ + 500 500 500 500 500 /* UG,C */ + 790 -260 500 790 500 /* UG,G */ + 500 500 500 500 -80 /* UG,U */ + 790 500 500 790 500 /* AU,E */ + 500 500 500 170 500 /* AU,A */ + 500 500 500 500 500 /* AU,C */ + 790 -260 500 790 500 /* AU,G */ + 500 500 500 500 -80 /* AU,U */ + 790 500 500 790 500 /* UA,E */ + 500 500 500 170 500 /* UA,A */ + 500 500 500 500 500 /* UA,C */ + 790 -260 500 790 500 /* UA,G */ + 500 500 500 500 -80 /* UA,U */ + 790 500 500 790 500 /* NS,E */ + 500 500 500 170 500 /* NS,A */ + 500 500 500 500 500 /* NS,C */ + 790 -260 500 790 500 /* NS,G */ + 500 500 500 500 -80 /* NS,U */ + +# mismatch_interior_1n + 0 0 0 0 0 /* CG,E */ + 0 0 0 0 0 /* CG,A */ + 0 0 0 0 0 /* CG,C */ + 0 0 0 0 0 /* CG,G */ + 0 0 0 0 0 /* CG,U */ + 0 0 0 0 0 /* GC,E */ + 0 0 0 0 0 /* GC,A */ + 0 0 0 0 0 /* GC,C */ + 0 0 0 0 0 /* GC,G */ + 0 0 0 0 0 /* GC,U */ + 70 70 70 70 70 /* GU,E */ + 70 70 70 70 70 /* GU,A */ + 70 70 70 70 70 /* GU,C */ + 70 70 70 70 70 /* GU,G */ + 70 70 70 70 70 /* GU,U */ + 70 70 70 70 70 /* UG,E */ + 70 70 70 70 70 /* UG,A */ + 70 70 70 70 70 /* UG,C */ + 70 70 70 70 70 /* UG,G */ + 70 70 70 70 70 /* UG,U */ + 70 70 70 70 70 /* AU,E */ + 70 70 70 70 70 /* AU,A */ + 70 70 70 70 70 /* AU,C */ + 70 70 70 70 70 /* AU,G */ + 70 70 70 70 70 /* AU,U */ + 70 70 70 70 70 /* UA,E */ + 70 70 70 70 70 /* UA,A */ + 70 70 70 70 70 /* UA,C */ + 70 70 70 70 70 /* UA,G */ + 70 70 70 70 70 /* UA,U */ + 70 70 70 70 70 /* NS,E */ + 70 70 70 70 70 /* NS,A */ + 70 70 70 70 70 /* NS,C */ + 70 70 70 70 70 /* NS,G */ + 70 70 70 70 70 /* NS,U */ + +# mismatch_interior_1n_enthalpies + 0 0 0 0 0 /* CG,E */ + 0 0 0 0 0 /* CG,A */ + 0 0 0 0 0 /* CG,C */ + 0 0 0 0 0 /* CG,G */ + 0 0 0 0 0 /* CG,U */ + 0 0 0 0 0 /* GC,E */ + 0 0 0 0 0 /* GC,A */ + 0 0 0 0 0 /* GC,C */ + 0 0 0 0 0 /* GC,G */ + 0 0 0 0 0 /* GC,U */ + 500 500 500 500 500 /* GU,E */ + 500 500 500 500 500 /* GU,A */ + 500 500 500 500 500 /* GU,C */ + 500 500 500 500 500 /* GU,G */ + 500 500 500 500 500 /* GU,U */ + 500 500 500 500 500 /* UG,E */ + 500 500 500 500 500 /* UG,A */ + 500 500 500 500 500 /* UG,C */ + 500 500 500 500 500 /* UG,G */ + 500 500 500 500 500 /* UG,U */ + 500 500 500 500 500 /* AU,E */ + 500 500 500 500 500 /* AU,A */ + 500 500 500 500 500 /* AU,C */ + 500 500 500 500 500 /* AU,G */ + 500 500 500 500 500 /* AU,U */ + 500 500 500 500 500 /* UA,E */ + 500 500 500 500 500 /* UA,A */ + 500 500 500 500 500 /* UA,C */ + 500 500 500 500 500 /* UA,G */ + 500 500 500 500 500 /* UA,U */ + 500 500 500 500 500 /* NS,E */ + 500 500 500 500 500 /* NS,A */ + 500 500 500 500 500 /* NS,C */ + 500 500 500 500 500 /* NS,G */ + 500 500 500 500 500 /* NS,U */ + +# mismatch_interior_23 + 0 0 0 0 0 /* CG,N */ + 0 0 0 -50 0 /* CG,A */ + 0 0 0 0 0 /* CG,C */ + 0 -110 0 -70 0 /* CG,G */ + 0 0 0 0 -30 /* CG,U */ + 0 0 0 0 0 /* GC,N */ + 0 0 0 0 0 /* GC,A */ + 0 0 0 0 0 /* GC,C */ + 0 -120 0 -70 0 /* GC,G */ + 0 0 0 0 -30 /* GC,U */ + 70 70 70 70 70 /* GU,N */ + 70 70 70 70 70 /* GU,A */ + 70 70 70 70 70 /* GU,C */ + 70 -40 70 0 70 /* GU,G */ + 70 70 70 70 40 /* GU,U */ + 70 70 70 70 70 /* UG,N */ + 70 70 70 20 70 /* UG,A */ + 70 70 70 70 70 /* UG,C */ + 70 -40 70 0 70 /* UG,G */ + 70 70 70 70 40 /* UG,U */ + 70 70 70 70 70 /* AU,N */ + 70 70 70 70 70 /* AU,A */ + 70 70 70 70 70 /* AU,C */ + 70 -40 70 0 70 /* AU,G */ + 70 70 70 70 40 /* AU,U */ + 70 70 70 70 70 /* UA,N */ + 70 70 70 20 70 /* UA,A */ + 70 70 70 70 70 /* UA,C */ + 70 -40 70 0 70 /* UA,G */ + 70 70 70 70 40 /* UA,U */ + 70 70 70 70 70 /* NN,N */ + 70 70 70 70 70 /* NN,A */ + 70 70 70 70 70 /* NN,C */ + 70 -40 70 0 70 /* NN,G */ + 70 70 70 70 40 /* NN,U */ + +# mismatch_interior_23_enthalpies + 0 0 0 0 0 /* CG,N */ + 0 0 0 -570 0 /* CG,A */ + 0 0 0 0 0 /* CG,C */ + 0 -860 0 -900 0 /* CG,G */ + 0 0 0 0 -640 /* CG,U */ + 0 0 0 0 0 /* GC,N */ + 0 0 0 0 0 /* GC,A */ + 0 0 0 0 0 /* GC,C */ + 0 -1090 0 -900 0 /* GC,G */ + 0 0 0 0 -640 /* GC,U */ + 500 500 500 500 500 /* GU,N */ + 500 500 500 500 500 /* GU,A */ + 500 500 500 500 500 /* GU,C */ + 500 -580 500 -400 500 /* GU,G */ + 500 500 500 500 -140 /* GU,U */ + 500 500 500 500 500 /* UG,N */ + 500 500 500 -60 500 /* UG,A */ + 500 500 500 500 500 /* UG,C */ + 500 -360 500 -400 500 /* UG,G */ + 500 500 500 500 -140 /* UG,U */ + 500 500 500 500 500 /* AU,N */ + 500 500 500 500 500 /* AU,A */ + 500 500 500 500 500 /* AU,C */ + 500 -580 500 -400 500 /* AU,G */ + 500 500 500 500 -140 /* AU,U */ + 500 500 500 500 500 /* UA,N */ + 500 500 500 -60 500 /* UA,A */ + 500 500 500 500 500 /* UA,C */ + 500 -360 500 -400 500 /* UA,G */ + 500 500 500 500 -140 /* UA,U */ + 500 500 500 500 500 /* NN,N */ + 500 500 500 500 500 /* NN,A */ + 500 500 500 500 500 /* NN,C */ + 500 -360 500 -400 500 /* NN,G */ + 500 500 500 500 -140 /* NN,U */ + +# mismatch_multi + -50 -110 -50 -140 -70 /* CG,N */ + -110 -110 -110 -160 -110 /* CG,A */ + -70 -150 -70 -150 -100 /* CG,C */ + -110 -130 -110 -140 -110 /* CG,G */ + -50 -150 -50 -150 -70 /* CG,U */ + -80 -140 -80 -140 -100 /* GC,N */ + -100 -150 -100 -140 -100 /* GC,A */ + -110 -150 -110 -150 -140 /* GC,C */ + -100 -140 -100 -160 -100 /* GC,G */ + -80 -150 -80 -150 -120 /* GC,U */ + -50 -80 -50 -50 -50 /* GU,N */ + -50 -100 -70 -50 -70 /* GU,A */ + -60 -80 -60 -80 -60 /* GU,C */ + -70 -110 -70 -80 -70 /* GU,G */ + -50 -80 -50 -80 -50 /* GU,U */ + -30 -30 -60 -60 -60 /* UG,N */ + -30 -30 -60 -60 -60 /* UG,A */ + -70 -100 -70 -100 -80 /* UG,C */ + -60 -80 -60 -80 -60 /* UG,G */ + -60 -100 -70 -100 -60 /* UG,U */ + -50 -80 -50 -80 -50 /* AU,N */ + -70 -100 -70 -110 -70 /* AU,A */ + -60 -80 -60 -80 -60 /* AU,C */ + -70 -110 -70 -120 -70 /* AU,G */ + -50 -80 -50 -80 -50 /* AU,U */ + -60 -80 -60 -80 -60 /* UA,N */ + -60 -80 -60 -80 -60 /* UA,A */ + -70 -100 -70 -100 -80 /* UA,C */ + -60 -80 -60 -80 -60 /* UA,G */ + -70 -100 -70 -100 -80 /* UA,U */ + -30 -30 -50 -50 -50 /* NN,N */ + -30 -30 -60 -50 -60 /* NN,A */ + -60 -80 -60 -80 -60 /* NN,C */ + -60 -80 -60 -80 -60 /* NN,G */ + -50 -80 -50 -80 -50 /* NN,U */ + +# mismatch_multi_enthalpies + 50 -400 50 -400 -30 /* CG,N */ + -520 -520 -720 -710 -720 /* CG,A */ + 50 -400 50 -400 -30 /* CG,C */ + -560 -560 -720 -620 -720 /* CG,G */ + -400 -400 -420 -400 -500 /* CG,U */ + -270 -560 -270 -560 -530 /* GC,N */ + -570 -910 -570 -820 -570 /* GC,A */ + -340 -560 -340 -560 -530 /* GC,C */ + -560 -560 -570 -920 -570 /* GC,G */ + -270 -560 -270 -560 -860 /* GC,U */ + 310 -480 -180 310 140 /* GU,N */ + 310 -480 -430 310 -430 /* GU,A */ + -140 -630 -510 -630 -140 /* GU,C */ + -150 -890 -430 -150 -430 /* GU,G */ + 140 -630 -180 -630 140 /* GU,U */ + 600 200 600 200 460 /* UG,N */ + -60 -340 -230 -60 -230 /* UG,A */ + 600 200 600 200 460 /* UG,C */ + -230 -350 -230 -350 -230 /* UG,G */ + 200 200 -30 200 160 /* UG,U */ + 140 -400 -180 -380 140 /* AU,N */ + -380 -400 -430 -380 -430 /* AU,A */ + -140 -630 -510 -630 -140 /* AU,C */ + -430 -890 -430 -890 -430 /* AU,G */ + 140 -630 -180 -630 140 /* AU,U */ + 600 200 600 200 460 /* UA,N */ + -230 -390 -230 -310 -230 /* UA,A */ + 600 200 600 200 460 /* UA,C */ + -230 -350 -230 -350 -230 /* UA,G */ + 200 200 -30 200 -170 /* UA,U */ + 600 200 600 310 460 /* NN,N */ + 310 -340 -230 310 -230 /* NN,A */ + 600 200 600 200 460 /* NN,C */ + -150 -350 -230 -150 -230 /* NN,G */ + 200 200 -30 200 160 /* NN,U */ + +# mismatch_exterior + -50 -110 -50 -140 -70 /* CG,N */ + -110 -110 -110 -160 -110 /* CG,A */ + -70 -150 -70 -150 -100 /* CG,C */ + -110 -130 -110 -140 -110 /* CG,G */ + -50 -150 -50 -150 -70 /* CG,U */ + -80 -140 -80 -140 -100 /* GC,N */ + -100 -150 -100 -140 -100 /* GC,A */ + -110 -150 -110 -150 -140 /* GC,C */ + -100 -140 -100 -160 -100 /* GC,G */ + -80 -150 -80 -150 -120 /* GC,U */ + -50 -80 -50 -50 -50 /* GU,N */ + -50 -100 -70 -50 -70 /* GU,A */ + -60 -80 -60 -80 -60 /* GU,C */ + -70 -110 -70 -80 -70 /* GU,G */ + -50 -80 -50 -80 -50 /* GU,U */ + -30 -30 -60 -60 -60 /* UG,N */ + -30 -30 -60 -60 -60 /* UG,A */ + -70 -100 -70 -100 -80 /* UG,C */ + -60 -80 -60 -80 -60 /* UG,G */ + -60 -100 -70 -100 -60 /* UG,U */ + -50 -80 -50 -80 -50 /* AU,N */ + -70 -100 -70 -110 -70 /* AU,A */ + -60 -80 -60 -80 -60 /* AU,C */ + -70 -110 -70 -120 -70 /* AU,G */ + -50 -80 -50 -80 -50 /* AU,U */ + -60 -80 -60 -80 -60 /* UA,N */ + -60 -80 -60 -80 -60 /* UA,A */ + -70 -100 -70 -100 -80 /* UA,C */ + -60 -80 -60 -80 -60 /* UA,G */ + -70 -100 -70 -100 -80 /* UA,U */ + -30 -30 -50 -50 -50 /* NN,N */ + -30 -30 -60 -50 -60 /* NN,A */ + -60 -80 -60 -80 -60 /* NN,C */ + -60 -80 -60 -80 -60 /* NN,G */ + -50 -80 -50 -80 -50 /* NN,U */ + +# mismatch_exterior_enthalpies + 50 -400 50 -400 -30 /* CG,N */ + -520 -520 -720 -710 -720 /* CG,A */ + 50 -400 50 -400 -30 /* CG,C */ + -560 -560 -720 -620 -720 /* CG,G */ + -400 -400 -420 -400 -500 /* CG,U */ + -270 -560 -270 -560 -530 /* GC,N */ + -570 -910 -570 -820 -570 /* GC,A */ + -340 -560 -340 -560 -530 /* GC,C */ + -560 -560 -570 -920 -570 /* GC,G */ + -270 -560 -270 -560 -860 /* GC,U */ + 310 -480 -180 310 140 /* GU,N */ + 310 -480 -430 310 -430 /* GU,A */ + -140 -630 -510 -630 -140 /* GU,C */ + -150 -890 -430 -150 -430 /* GU,G */ + 140 -630 -180 -630 140 /* GU,U */ + 600 200 600 200 460 /* UG,N */ + -60 -340 -230 -60 -230 /* UG,A */ + 600 200 600 200 460 /* UG,C */ + -230 -350 -230 -350 -230 /* UG,G */ + 200 200 -30 200 160 /* UG,U */ + 140 -400 -180 -380 140 /* AU,N */ + -380 -400 -430 -380 -430 /* AU,A */ + -140 -630 -510 -630 -140 /* AU,C */ + -430 -890 -430 -890 -430 /* AU,G */ + 140 -630 -180 -630 140 /* AU,U */ + 600 200 600 200 460 /* UA,N */ + -230 -390 -230 -310 -230 /* UA,A */ + 600 200 600 200 460 /* UA,C */ + -230 -350 -230 -350 -230 /* UA,G */ + 200 200 -30 200 -170 /* UA,U */ + 600 200 600 310 460 /* NN,N */ + 310 -340 -230 310 -230 /* NN,A */ + 600 200 600 200 460 /* NN,C */ + -150 -350 -230 -150 -230 /* NN,G */ + 200 200 -30 200 160 /* NN,U */ + +# dangle5 +/* N A C G U */ + -10 -50 -30 -20 -10 /* CG */ + -0 -20 -30 -0 -0 /* GC */ + -20 -30 -30 -40 -20 /* GU */ + -10 -30 -10 -20 -20 /* UG */ + -20 -30 -30 -40 -20 /* AU */ + -10 -30 -10 -20 -20 /* UA */ + -0 -20 -10 -0 -0 /* NN */ + +# dangle5_enthalpies +/* N A C G U */ + 330 -240 330 80 -140 /* CG */ + 70 -160 70 -460 -40 /* GC */ + 310 160 220 70 310 /* GU */ + 690 -50 690 60 60 /* UG */ + 310 160 220 70 310 /* AU */ + 690 -50 690 60 60 /* UA */ + 690 160 690 80 310 /* NN */ + +# dangle3 +/* N A C G U */ + -40 -110 -40 -130 -60 /* CG */ + -80 -170 -80 -170 -120 /* GC */ + -10 -70 -10 -70 -10 /* GU */ + -50 -80 -50 -80 -60 /* UG */ + -10 -70 -10 -70 -10 /* AU */ + -50 -80 -50 -80 -60 /* UA */ + -10 -70 -10 -70 -10 /* NN */ + +# dangle3_enthalpies +/* N A C G U */ + -280 -740 -280 -640 -360 /* CG */ + -410 -900 -410 -860 -750 /* GC */ + -70 -570 -70 -580 -220 /* GU */ + -90 -490 -90 -550 -230 /* UG */ + -70 -570 -70 -580 -220 /* AU */ + -90 -490 -90 -550 -230 /* UA */ + -70 -490 -70 -550 -220 /* NN */ + +# int11 + 90 90 50 50 50 /* CG,CG,N */ + 90 90 50 50 50 /* CG,CG,A */ + 50 50 50 50 50 /* CG,CG,C */ + 50 50 50 -140 50 /* CG,CG,G */ + 50 50 50 50 40 /* CG,CG,U */ + 90 90 50 50 60 /* CG,GC,N */ + 90 90 -40 50 50 /* CG,GC,A */ + 60 30 50 50 60 /* CG,GC,C */ + 50 -10 50 -220 50 /* CG,GC,G */ + 50 50 0 50 -10 /* CG,GC,U */ + 120 120 120 120 120 /* CG,GU,N */ + 120 60 50 120 120 /* CG,GU,A */ + 120 120 120 120 120 /* CG,GU,C */ + 120 -20 120 -140 120 /* CG,GU,G */ + 120 120 100 120 110 /* CG,GU,U */ + 220 220 170 120 120 /* CG,UG,N */ + 220 220 130 120 120 /* CG,UG,A */ + 170 120 170 120 120 /* CG,UG,C */ + 120 120 120 -140 120 /* CG,UG,G */ + 120 120 120 120 110 /* CG,UG,U */ + 120 120 120 120 120 /* CG,AU,N */ + 120 120 120 120 120 /* CG,AU,A */ + 120 120 120 120 120 /* CG,AU,C */ + 120 120 120 -140 120 /* CG,AU,G */ + 120 120 120 120 80 /* CG,AU,U */ + 120 120 120 120 120 /* CG,UA,N */ + 120 120 120 120 120 /* CG,UA,A */ + 120 120 120 120 120 /* CG,UA,C */ + 120 120 120 -140 120 /* CG,UA,G */ + 120 120 120 120 120 /* CG,UA,U */ + 220 220 170 120 120 /* CG,NN,N */ + 220 220 130 120 120 /* CG,NN,A */ + 170 120 170 120 120 /* CG,NN,C */ + 120 120 120 -140 120 /* CG,NN,G */ + 120 120 120 120 120 /* CG,NN,U */ + 90 90 60 50 50 /* GC,CG,N */ + 90 90 30 -10 50 /* GC,CG,A */ + 50 -40 50 50 0 /* GC,CG,C */ + 50 50 50 -220 50 /* GC,CG,G */ + 60 50 60 50 -10 /* GC,CG,U */ + 80 80 50 50 50 /* GC,GC,N */ + 80 80 50 50 50 /* GC,GC,A */ + 50 50 50 50 50 /* GC,GC,C */ + 50 50 50 -230 50 /* GC,GC,G */ + 50 50 50 50 -60 /* GC,GC,U */ + 190 190 120 150 150 /* GC,GU,N */ + 190 190 120 150 120 /* GC,GU,A */ + 120 120 120 120 120 /* GC,GU,C */ + 120 120 120 -140 120 /* GC,GU,G */ + 150 120 120 120 150 /* GC,GU,U */ + 160 160 120 120 120 /* GC,UG,N */ + 160 160 120 100 120 /* GC,UG,A */ + 120 120 120 120 120 /* GC,UG,C */ + 120 120 120 -140 120 /* GC,UG,G */ + 120 120 120 120 70 /* GC,UG,U */ + 120 120 120 120 120 /* GC,AU,N */ + 120 120 120 120 120 /* GC,AU,A */ + 120 120 120 120 120 /* GC,AU,C */ + 120 120 120 -140 120 /* GC,AU,G */ + 120 120 120 120 80 /* GC,AU,U */ + 120 120 120 120 120 /* GC,UA,N */ + 120 120 120 120 120 /* GC,UA,A */ + 120 120 120 120 120 /* GC,UA,C */ + 120 120 120 -140 120 /* GC,UA,G */ + 120 120 120 120 120 /* GC,UA,U */ + 190 190 120 150 150 /* GC,NN,N */ + 190 190 120 150 120 /* GC,NN,A */ + 120 120 120 120 120 /* GC,NN,C */ + 120 120 120 -140 120 /* GC,NN,G */ + 150 120 120 120 150 /* GC,NN,U */ + 120 120 120 120 120 /* GU,CG,N */ + 120 60 120 -20 120 /* GU,CG,A */ + 120 50 120 120 100 /* GU,CG,C */ + 120 120 120 -140 120 /* GU,CG,G */ + 120 120 120 120 110 /* GU,CG,U */ + 190 190 120 120 150 /* GU,GC,N */ + 190 190 120 120 120 /* GU,GC,A */ + 120 120 120 120 120 /* GU,GC,C */ + 150 150 120 -140 120 /* GU,GC,G */ + 150 120 120 120 150 /* GU,GC,U */ + 190 190 190 190 190 /* GU,GU,N */ + 190 190 190 190 190 /* GU,GU,A */ + 190 190 190 190 190 /* GU,GU,C */ + 190 190 190 -70 190 /* GU,GU,G */ + 190 190 190 190 120 /* GU,GU,U */ + 190 190 190 190 190 /* GU,UG,N */ + 190 190 190 190 190 /* GU,UG,A */ + 190 190 190 190 190 /* GU,UG,C */ + 190 190 190 -70 190 /* GU,UG,G */ + 190 190 190 190 160 /* GU,UG,U */ + 190 190 190 190 190 /* GU,AU,N */ + 190 190 190 190 190 /* GU,AU,A */ + 190 190 190 190 190 /* GU,AU,C */ + 190 190 190 -70 190 /* GU,AU,G */ + 190 190 190 190 120 /* GU,AU,U */ + 190 190 190 190 190 /* GU,UA,N */ + 190 190 190 190 190 /* GU,UA,A */ + 190 190 190 190 190 /* GU,UA,C */ + 190 190 190 -70 190 /* GU,UA,G */ + 190 190 190 190 160 /* GU,UA,U */ + 190 190 190 190 190 /* GU,NN,N */ + 190 190 190 190 190 /* GU,NN,A */ + 190 190 190 190 190 /* GU,NN,C */ + 190 190 190 -70 190 /* GU,NN,G */ + 190 190 190 190 160 /* GU,NN,U */ + 220 220 170 120 120 /* UG,CG,N */ + 220 220 120 120 120 /* UG,CG,A */ + 170 130 170 120 120 /* UG,CG,C */ + 120 120 120 -140 120 /* UG,CG,G */ + 120 120 120 120 110 /* UG,CG,U */ + 160 160 120 120 120 /* UG,GC,N */ + 160 160 120 120 120 /* UG,GC,A */ + 120 120 120 120 120 /* UG,GC,C */ + 120 100 120 -140 120 /* UG,GC,G */ + 120 120 120 120 70 /* UG,GC,U */ + 190 190 190 190 190 /* UG,GU,N */ + 190 190 190 190 190 /* UG,GU,A */ + 190 190 190 190 190 /* UG,GU,C */ + 190 190 190 -70 190 /* UG,GU,G */ + 190 190 190 190 160 /* UG,GU,U */ + 190 190 190 190 190 /* UG,UG,N */ + 190 190 190 190 190 /* UG,UG,A */ + 190 190 190 190 190 /* UG,UG,C */ + 190 190 190 -70 190 /* UG,UG,G */ + 190 190 190 190 190 /* UG,UG,U */ + 190 190 190 190 190 /* UG,AU,N */ + 190 190 190 190 190 /* UG,AU,A */ + 190 190 190 190 190 /* UG,AU,C */ + 190 190 190 -70 190 /* UG,AU,G */ + 190 190 190 190 160 /* UG,AU,U */ + 190 190 190 190 190 /* UG,UA,N */ + 190 190 190 190 190 /* UG,UA,A */ + 190 190 190 190 190 /* UG,UA,C */ + 190 190 190 -70 190 /* UG,UA,G */ + 190 190 190 190 190 /* UG,UA,U */ + 220 220 190 190 190 /* UG,NN,N */ + 220 220 190 190 190 /* UG,NN,A */ + 190 190 190 190 190 /* UG,NN,C */ + 190 190 190 -70 190 /* UG,NN,G */ + 190 190 190 190 190 /* UG,NN,U */ + 120 120 120 120 120 /* AU,CG,N */ + 120 120 120 120 120 /* AU,CG,A */ + 120 120 120 120 120 /* AU,CG,C */ + 120 120 120 -140 120 /* AU,CG,G */ + 120 120 120 120 80 /* AU,CG,U */ + 120 120 120 120 120 /* AU,GC,N */ + 120 120 120 120 120 /* AU,GC,A */ + 120 120 120 120 120 /* AU,GC,C */ + 120 120 120 -140 120 /* AU,GC,G */ + 120 120 120 120 80 /* AU,GC,U */ + 190 190 190 190 190 /* AU,GU,N */ + 190 190 190 190 190 /* AU,GU,A */ + 190 190 190 190 190 /* AU,GU,C */ + 190 190 190 -70 190 /* AU,GU,G */ + 190 190 190 190 120 /* AU,GU,U */ + 190 190 190 190 190 /* AU,UG,N */ + 190 190 190 190 190 /* AU,UG,A */ + 190 190 190 190 190 /* AU,UG,C */ + 190 190 190 -70 190 /* AU,UG,G */ + 190 190 190 190 160 /* AU,UG,U */ + 190 190 190 190 190 /* AU,AU,N */ + 190 190 190 190 190 /* AU,AU,A */ + 190 190 190 190 190 /* AU,AU,C */ + 190 190 190 -70 190 /* AU,AU,G */ + 190 190 190 190 120 /* AU,AU,U */ + 190 190 190 190 190 /* AU,UA,N */ + 190 190 190 190 190 /* AU,UA,A */ + 190 190 190 190 190 /* AU,UA,C */ + 190 190 190 -70 190 /* AU,UA,G */ + 190 190 190 190 150 /* AU,UA,U */ + 190 190 190 190 190 /* AU,NN,N */ + 190 190 190 190 190 /* AU,NN,A */ + 190 190 190 190 190 /* AU,NN,C */ + 190 190 190 -70 190 /* AU,NN,G */ + 190 190 190 190 160 /* AU,NN,U */ + 120 120 120 120 120 /* UA,CG,N */ + 120 120 120 120 120 /* UA,CG,A */ + 120 120 120 120 120 /* UA,CG,C */ + 120 120 120 -140 120 /* UA,CG,G */ + 120 120 120 120 120 /* UA,CG,U */ + 120 120 120 120 120 /* UA,GC,N */ + 120 120 120 120 120 /* UA,GC,A */ + 120 120 120 120 120 /* UA,GC,C */ + 120 120 120 -140 120 /* UA,GC,G */ + 120 120 120 120 120 /* UA,GC,U */ + 190 190 190 190 190 /* UA,GU,N */ + 190 190 190 190 190 /* UA,GU,A */ + 190 190 190 190 190 /* UA,GU,C */ + 190 190 190 -70 190 /* UA,GU,G */ + 190 190 190 190 160 /* UA,GU,U */ + 190 190 190 190 190 /* UA,UG,N */ + 190 190 190 190 190 /* UA,UG,A */ + 190 190 190 190 190 /* UA,UG,C */ + 190 190 190 -70 190 /* UA,UG,G */ + 190 190 190 190 190 /* UA,UG,U */ + 190 190 190 190 190 /* UA,AU,N */ + 190 190 190 190 190 /* UA,AU,A */ + 190 190 190 190 190 /* UA,AU,C */ + 190 190 190 -70 190 /* UA,AU,G */ + 190 190 190 190 150 /* UA,AU,U */ + 190 190 190 190 190 /* UA,UA,N */ + 190 190 190 190 190 /* UA,UA,A */ + 190 190 190 190 190 /* UA,UA,C */ + 190 190 190 -70 190 /* UA,UA,G */ + 190 190 190 190 170 /* UA,UA,U */ + 190 190 190 190 190 /* UA,NN,N */ + 190 190 190 190 190 /* UA,NN,A */ + 190 190 190 190 190 /* UA,NN,C */ + 190 190 190 -70 190 /* UA,NN,G */ + 190 190 190 190 190 /* UA,NN,U */ + 220 220 170 120 120 /* NN,CG,N */ + 220 220 120 120 120 /* NN,CG,A */ + 170 130 170 120 120 /* NN,CG,C */ + 120 120 120 -140 120 /* NN,CG,G */ + 120 120 120 120 120 /* NN,CG,U */ + 190 190 120 120 150 /* NN,GC,N */ + 190 190 120 120 120 /* NN,GC,A */ + 120 120 120 120 120 /* NN,GC,C */ + 150 150 120 -140 120 /* NN,GC,G */ + 150 120 120 120 150 /* NN,GC,U */ + 190 190 190 190 190 /* NN,GU,N */ + 190 190 190 190 190 /* NN,GU,A */ + 190 190 190 190 190 /* NN,GU,C */ + 190 190 190 -70 190 /* NN,GU,G */ + 190 190 190 190 160 /* NN,GU,U */ + 220 220 190 190 190 /* NN,UG,N */ + 220 220 190 190 190 /* NN,UG,A */ + 190 190 190 190 190 /* NN,UG,C */ + 190 190 190 -70 190 /* NN,UG,G */ + 190 190 190 190 190 /* NN,UG,U */ + 190 190 190 190 190 /* NN,AU,N */ + 190 190 190 190 190 /* NN,AU,A */ + 190 190 190 190 190 /* NN,AU,C */ + 190 190 190 -70 190 /* NN,AU,G */ + 190 190 190 190 160 /* NN,AU,U */ + 190 190 190 190 190 /* NN,UA,N */ + 190 190 190 190 190 /* NN,UA,A */ + 190 190 190 190 190 /* NN,UA,C */ + 190 190 190 -70 190 /* NN,UA,G */ + 190 190 190 190 190 /* NN,UA,U */ + 220 220 190 190 190 /* NN,NN,N */ + 220 220 190 190 190 /* NN,NN,A */ + 190 190 190 190 190 /* NN,NN,C */ + 190 190 190 -70 190 /* NN,NN,G */ + 190 190 190 190 190 /* NN,NN,U */ + +# int11_enthalpies + -1050 -1050 -1050 -1050 -1050 /* CG,CG,N */ + -1050 -1050 -1050 -1050 -1050 /* CG,CG,A */ + -1050 -1050 -1050 -1050 -1050 /* CG,CG,C */ + -1050 -1050 -1050 -1840 -1050 /* CG,CG,G */ + -1050 -1050 -1050 -1050 -1050 /* CG,CG,U */ + -1050 -1050 -1050 -1050 -1050 /* CG,GC,N */ + -1050 -1050 -1050 -1050 -1050 /* CG,GC,A */ + -1050 -1050 -1050 -1050 -1050 /* CG,GC,C */ + -1050 -1050 -1050 -1840 -1050 /* CG,GC,G */ + -1050 -1050 -1050 -1050 -1390 /* CG,GC,U */ + -550 -550 -550 -550 -550 /* CG,GU,N */ + -550 -550 -550 -550 -550 /* CG,GU,A */ + -550 -550 -550 -550 -550 /* CG,GU,C */ + -550 -550 -550 -1340 -550 /* CG,GU,G */ + -550 -550 -550 -550 -890 /* CG,GU,U */ + -550 -550 -550 -550 -550 /* CG,UG,N */ + -550 -550 -550 -550 -550 /* CG,UG,A */ + -550 -550 -550 -550 -550 /* CG,UG,C */ + -550 -550 -550 -1340 -550 /* CG,UG,G */ + -550 -550 -550 -550 -550 /* CG,UG,U */ + -550 -550 -550 -550 -550 /* CG,AU,N */ + -550 -550 -550 -550 -550 /* CG,AU,A */ + -550 -550 -550 -550 -550 /* CG,AU,C */ + -550 -550 -550 -1340 -550 /* CG,AU,G */ + -550 -550 -550 -550 -890 /* CG,AU,U */ + -550 -550 -550 -550 -550 /* CG,UA,N */ + -550 -550 -550 -550 -550 /* CG,UA,A */ + -550 -550 -550 -550 -550 /* CG,UA,C */ + -550 -550 -550 -1340 -550 /* CG,UA,G */ + -550 -550 -550 -550 -550 /* CG,UA,U */ + -550 -550 -550 -550 -550 /* CG,NN,N */ + -550 -550 -550 -550 -550 /* CG,NN,A */ + -550 -550 -550 -550 -550 /* CG,NN,C */ + -550 -550 -550 -1340 -550 /* CG,NN,G */ + -550 -550 -550 -550 -550 /* CG,NN,U */ + -1050 -1050 -1050 -1050 -1050 /* GC,CG,N */ + -1050 -1050 -1050 -1050 -1050 /* GC,CG,A */ + -1050 -1050 -1050 -1050 -1050 /* GC,CG,C */ + -1050 -1050 -1050 -1840 -1050 /* GC,CG,G */ + -1050 -1050 -1050 -1050 -1390 /* GC,CG,U */ + -1050 -1050 -1050 -1050 -1050 /* GC,GC,N */ + -1050 -1050 -1050 -1050 -1050 /* GC,GC,A */ + -1050 -1050 -1050 -1050 -1050 /* GC,GC,C */ + -1050 -1050 -1050 -1840 -1050 /* GC,GC,G */ + -1050 -1050 -1050 -1050 -1730 /* GC,GC,U */ + -550 -550 -550 -550 -550 /* GC,GU,N */ + -550 -550 -550 -550 -550 /* GC,GU,A */ + -550 -550 -550 -550 -550 /* GC,GU,C */ + -550 -550 -550 -1340 -550 /* GC,GU,G */ + -550 -550 -550 -550 -1230 /* GC,GU,U */ + -550 -550 -550 -550 -550 /* GC,UG,N */ + -550 -550 -550 -550 -550 /* GC,UG,A */ + -550 -550 -550 -550 -550 /* GC,UG,C */ + -550 -550 -550 -1340 -550 /* GC,UG,G */ + -550 -550 -550 -550 -890 /* GC,UG,U */ + -550 -550 -550 -550 -550 /* GC,AU,N */ + -550 -550 -550 -550 -550 /* GC,AU,A */ + -550 -550 -550 -550 -550 /* GC,AU,C */ + -550 -550 -550 -1340 -550 /* GC,AU,G */ + -550 -550 -550 -550 -1230 /* GC,AU,U */ + -550 -550 -550 -550 -550 /* GC,UA,N */ + -550 -550 -550 -550 -550 /* GC,UA,A */ + -550 -550 -550 -550 -550 /* GC,UA,C */ + -550 -550 -550 -1340 -550 /* GC,UA,G */ + -550 -550 -550 -550 -890 /* GC,UA,U */ + -550 -550 -550 -550 -550 /* GC,NN,N */ + -550 -550 -550 -550 -550 /* GC,NN,A */ + -550 -550 -550 -550 -550 /* GC,NN,C */ + -550 -550 -550 -1340 -550 /* GC,NN,G */ + -550 -550 -550 -550 -890 /* GC,NN,U */ + -550 -550 -550 -550 -550 /* GU,CG,N */ + -550 -550 -550 -550 -550 /* GU,CG,A */ + -550 -550 -550 -550 -550 /* GU,CG,C */ + -550 -550 -550 -1340 -550 /* GU,CG,G */ + -550 -550 -550 -550 -890 /* GU,CG,U */ + -550 -550 -550 -550 -550 /* GU,GC,N */ + -550 -550 -550 -550 -550 /* GU,GC,A */ + -550 -550 -550 -550 -550 /* GU,GC,C */ + -550 -550 -550 -1340 -550 /* GU,GC,G */ + -550 -550 -550 -550 -1230 /* GU,GC,U */ + -50 -50 -50 -50 -50 /* GU,GU,N */ + -50 -50 -50 -50 -50 /* GU,GU,A */ + -50 -50 -50 -50 -50 /* GU,GU,C */ + -50 -50 -50 -830 -50 /* GU,GU,G */ + -50 -50 -50 -50 -730 /* GU,GU,U */ + -50 -50 -50 -50 -50 /* GU,UG,N */ + -50 -50 -50 -50 -50 /* GU,UG,A */ + -50 -50 -50 -50 -50 /* GU,UG,C */ + -50 -50 -50 -830 -50 /* GU,UG,G */ + -50 -50 -50 -50 -390 /* GU,UG,U */ + -50 -50 -50 -50 -50 /* GU,AU,N */ + -50 -50 -50 -50 -50 /* GU,AU,A */ + -50 -50 -50 -50 -50 /* GU,AU,C */ + -50 -50 -50 -830 -50 /* GU,AU,G */ + -50 -50 -50 -50 -730 /* GU,AU,U */ + -50 -50 -50 -50 -50 /* GU,UA,N */ + -50 -50 -50 -50 -50 /* GU,UA,A */ + -50 -50 -50 -50 -50 /* GU,UA,C */ + -50 -50 -50 -830 -50 /* GU,UA,G */ + -50 -50 -50 -50 -390 /* GU,UA,U */ + -50 -50 -50 -50 -50 /* GU,NN,N */ + -50 -50 -50 -50 -50 /* GU,NN,A */ + -50 -50 -50 -50 -50 /* GU,NN,C */ + -50 -50 -50 -830 -50 /* GU,NN,G */ + -50 -50 -50 -50 -390 /* GU,NN,U */ + -550 -550 -550 -550 -550 /* UG,CG,N */ + -550 -550 -550 -550 -550 /* UG,CG,A */ + -550 -550 -550 -550 -550 /* UG,CG,C */ + -550 -550 -550 -1340 -550 /* UG,CG,G */ + -550 -550 -550 -550 -550 /* UG,CG,U */ + -550 -550 -550 -550 -550 /* UG,GC,N */ + -550 -550 -550 -550 -550 /* UG,GC,A */ + -550 -550 -550 -550 -550 /* UG,GC,C */ + -550 -550 -550 -1340 -550 /* UG,GC,G */ + -550 -550 -550 -550 -890 /* UG,GC,U */ + -50 -50 -50 -50 -50 /* UG,GU,N */ + -50 -50 -50 -50 -50 /* UG,GU,A */ + -50 -50 -50 -50 -50 /* UG,GU,C */ + -50 -50 -50 -830 -50 /* UG,GU,G */ + -50 -50 -50 -50 -390 /* UG,GU,U */ + -50 -50 -50 -50 -50 /* UG,UG,N */ + -50 -50 -50 -50 -50 /* UG,UG,A */ + -50 -50 -50 -50 -50 /* UG,UG,C */ + -50 -50 -50 -830 -50 /* UG,UG,G */ + -50 -50 -50 -50 -50 /* UG,UG,U */ + -50 -50 -50 -50 -50 /* UG,AU,N */ + -50 -50 -50 -50 -50 /* UG,AU,A */ + -50 -50 -50 -50 -50 /* UG,AU,C */ + -50 -50 -50 -830 -50 /* UG,AU,G */ + -50 -50 -50 -50 -390 /* UG,AU,U */ + -50 -50 -50 -50 -50 /* UG,UA,N */ + -50 -50 -50 -50 -50 /* UG,UA,A */ + -50 -50 -50 -50 -50 /* UG,UA,C */ + -50 -50 -50 -830 -50 /* UG,UA,G */ + -50 -50 -50 -50 -50 /* UG,UA,U */ + -50 -50 -50 -50 -50 /* UG,NN,N */ + -50 -50 -50 -50 -50 /* UG,NN,A */ + -50 -50 -50 -50 -50 /* UG,NN,C */ + -50 -50 -50 -830 -50 /* UG,NN,G */ + -50 -50 -50 -50 -50 /* UG,NN,U */ + -550 -550 -550 -550 -550 /* AU,CG,N */ + -550 -550 -550 -550 -550 /* AU,CG,A */ + -550 -550 -550 -550 -550 /* AU,CG,C */ + -550 -550 -550 -1340 -550 /* AU,CG,G */ + -550 -550 -550 -550 -890 /* AU,CG,U */ + -550 -550 -550 -550 -550 /* AU,GC,N */ + -550 -550 -550 -550 -550 /* AU,GC,A */ + -550 -550 -550 -550 -550 /* AU,GC,C */ + -550 -550 -550 -1340 -550 /* AU,GC,G */ + -550 -550 -550 -550 -1230 /* AU,GC,U */ + -50 -50 -50 -50 -50 /* AU,GU,N */ + -50 -50 -50 -50 -50 /* AU,GU,A */ + -50 -50 -50 -50 -50 /* AU,GU,C */ + -50 -50 -50 -830 -50 /* AU,GU,G */ + -50 -50 -50 -50 -730 /* AU,GU,U */ + -50 -50 -50 -50 -50 /* AU,UG,N */ + -50 -50 -50 -50 -50 /* AU,UG,A */ + -50 -50 -50 -50 -50 /* AU,UG,C */ + -50 -50 -50 -830 -50 /* AU,UG,G */ + -50 -50 -50 -50 -390 /* AU,UG,U */ + -50 -50 -50 -50 -50 /* AU,AU,N */ + -50 -50 -50 -50 -50 /* AU,AU,A */ + -50 -50 -50 -50 -50 /* AU,AU,C */ + -50 -50 -50 -830 -50 /* AU,AU,G */ + -50 -50 -50 -50 -730 /* AU,AU,U */ + -50 -50 -50 -50 -50 /* AU,UA,N */ + -50 -50 -50 -50 -50 /* AU,UA,A */ + -50 -50 -50 -50 -50 /* AU,UA,C */ + -50 -50 -50 -830 -50 /* AU,UA,G */ + -50 -50 -50 -50 -390 /* AU,UA,U */ + -50 -50 -50 -50 -50 /* AU,NN,N */ + -50 -50 -50 -50 -50 /* AU,NN,A */ + -50 -50 -50 -50 -50 /* AU,NN,C */ + -50 -50 -50 -830 -50 /* AU,NN,G */ + -50 -50 -50 -50 -390 /* AU,NN,U */ + -550 -550 -550 -550 -550 /* UA,CG,N */ + -550 -550 -550 -550 -550 /* UA,CG,A */ + -550 -550 -550 -550 -550 /* UA,CG,C */ + -550 -550 -550 -1340 -550 /* UA,CG,G */ + -550 -550 -550 -550 -550 /* UA,CG,U */ + -550 -550 -550 -550 -550 /* UA,GC,N */ + -550 -550 -550 -550 -550 /* UA,GC,A */ + -550 -550 -550 -550 -550 /* UA,GC,C */ + -550 -550 -550 -1340 -550 /* UA,GC,G */ + -550 -550 -550 -550 -890 /* UA,GC,U */ + -50 -50 -50 -50 -50 /* UA,GU,N */ + -50 -50 -50 -50 -50 /* UA,GU,A */ + -50 -50 -50 -50 -50 /* UA,GU,C */ + -50 -50 -50 -830 -50 /* UA,GU,G */ + -50 -50 -50 -50 -390 /* UA,GU,U */ + -50 -50 -50 -50 -50 /* UA,UG,N */ + -50 -50 -50 -50 -50 /* UA,UG,A */ + -50 -50 -50 -50 -50 /* UA,UG,C */ + -50 -50 -50 -830 -50 /* UA,UG,G */ + -50 -50 -50 -50 -50 /* UA,UG,U */ + -50 -50 -50 -50 -50 /* UA,AU,N */ + -50 -50 -50 -50 -50 /* UA,AU,A */ + -50 -50 -50 -50 -50 /* UA,AU,C */ + -50 -50 -50 -830 -50 /* UA,AU,G */ + -50 -50 -50 -50 -390 /* UA,AU,U */ + -50 -50 -50 -50 -50 /* UA,UA,N */ + -50 -50 -50 -50 -50 /* UA,UA,A */ + -50 -50 -50 -50 -50 /* UA,UA,C */ + -50 -50 -50 -830 -50 /* UA,UA,G */ + -50 -50 -50 -50 -50 /* UA,UA,U */ + -50 -50 -50 -50 -50 /* UA,NN,N */ + -50 -50 -50 -50 -50 /* UA,NN,A */ + -50 -50 -50 -50 -50 /* UA,NN,C */ + -50 -50 -50 -830 -50 /* UA,NN,G */ + -50 -50 -50 -50 -50 /* UA,NN,U */ + -550 -550 -550 -550 -550 /* NN,CG,N */ + -550 -550 -550 -550 -550 /* NN,CG,A */ + -550 -550 -550 -550 -550 /* NN,CG,C */ + -550 -550 -550 -1340 -550 /* NN,CG,G */ + -550 -550 -550 -550 -550 /* NN,CG,U */ + -550 -550 -550 -550 -550 /* NN,GC,N */ + -550 -550 -550 -550 -550 /* NN,GC,A */ + -550 -550 -550 -550 -550 /* NN,GC,C */ + -550 -550 -550 -1340 -550 /* NN,GC,G */ + -550 -550 -550 -550 -890 /* NN,GC,U */ + -50 -50 -50 -50 -50 /* NN,GU,N */ + -50 -50 -50 -50 -50 /* NN,GU,A */ + -50 -50 -50 -50 -50 /* NN,GU,C */ + -50 -50 -50 -830 -50 /* NN,GU,G */ + -50 -50 -50 -50 -390 /* NN,GU,U */ + -50 -50 -50 -50 -50 /* NN,UG,N */ + -50 -50 -50 -50 -50 /* NN,UG,A */ + -50 -50 -50 -50 -50 /* NN,UG,C */ + -50 -50 -50 -830 -50 /* NN,UG,G */ + -50 -50 -50 -50 -50 /* NN,UG,U */ + -50 -50 -50 -50 -50 /* NN,AU,N */ + -50 -50 -50 -50 -50 /* NN,AU,A */ + -50 -50 -50 -50 -50 /* NN,AU,C */ + -50 -50 -50 -830 -50 /* NN,AU,G */ + -50 -50 -50 -50 -390 /* NN,AU,U */ + -50 -50 -50 -50 -50 /* NN,UA,N */ + -50 -50 -50 -50 -50 /* NN,UA,A */ + -50 -50 -50 -50 -50 /* NN,UA,C */ + -50 -50 -50 -830 -50 /* NN,UA,G */ + -50 -50 -50 -50 -50 /* NN,UA,U */ + -50 -50 -50 -50 -50 /* NN,NN,N */ + -50 -50 -50 -50 -50 /* NN,NN,A */ + -50 -50 -50 -50 -50 /* NN,NN,C */ + -50 -50 -50 -830 -50 /* NN,NN,G */ + -50 -50 -50 -50 -50 /* NN,NN,U */ + +# int21 + 230 230 230 230 230 /* CG,CG,N,N */ + 230 230 230 230 230 /* CG,CG,N,A */ + 230 230 230 230 230 /* CG,CG,N,C */ + 230 230 230 230 230 /* CG,CG,N,G */ + 230 230 230 230 230 /* CG,CG,N,U */ + 230 230 230 110 230 /* CG,CG,A,N */ + 230 230 230 110 230 /* CG,CG,A,A */ + 230 230 230 110 230 /* CG,CG,A,C */ + 110 110 110 110 110 /* CG,CG,A,G */ + 230 230 230 110 230 /* CG,CG,A,U */ + 230 230 230 230 230 /* CG,CG,C,N */ + 230 230 230 230 230 /* CG,CG,C,A */ + 230 230 230 230 230 /* CG,CG,C,C */ + 230 230 230 230 230 /* CG,CG,C,G */ + 230 230 230 230 230 /* CG,CG,C,U */ + 230 110 230 110 230 /* CG,CG,G,N */ + 110 110 110 110 110 /* CG,CG,G,A */ + 230 110 230 110 230 /* CG,CG,G,C */ + 110 110 110 110 110 /* CG,CG,G,G */ + 230 110 230 110 230 /* CG,CG,G,U */ + 230 230 230 230 150 /* CG,CG,U,N */ + 230 230 230 230 150 /* CG,CG,U,A */ + 230 230 230 230 150 /* CG,CG,U,C */ + 230 230 230 230 150 /* CG,CG,U,G */ + 150 150 150 150 150 /* CG,CG,U,U */ + 250 250 250 230 230 /* CG,GC,N,N */ + 250 250 230 230 230 /* CG,GC,N,A */ + 250 230 250 230 230 /* CG,GC,N,C */ + 230 230 230 230 230 /* CG,GC,N,G */ + 250 250 230 230 230 /* CG,GC,N,U */ + 250 250 230 110 230 /* CG,GC,A,N */ + 250 250 230 110 230 /* CG,GC,A,A */ + 230 230 170 110 230 /* CG,GC,A,C */ + 110 80 110 110 110 /* CG,GC,A,G */ + 230 230 230 110 230 /* CG,GC,A,U */ + 250 250 250 230 230 /* CG,GC,C,N */ + 230 230 230 230 230 /* CG,GC,C,A */ + 250 230 250 230 230 /* CG,GC,C,C */ + 230 230 230 230 230 /* CG,GC,C,G */ + 250 250 230 230 230 /* CG,GC,C,U */ + 230 170 230 110 230 /* CG,GC,G,N */ + 230 170 230 80 230 /* CG,GC,G,A */ + 230 110 230 110 230 /* CG,GC,G,C */ + 120 120 110 110 110 /* CG,GC,G,G */ + 230 110 230 110 230 /* CG,GC,G,U */ + 230 230 230 230 150 /* CG,GC,U,N */ + 230 230 230 230 150 /* CG,GC,U,A */ + 230 230 220 230 150 /* CG,GC,U,C */ + 230 230 230 230 150 /* CG,GC,U,G */ + 170 150 170 150 140 /* CG,GC,U,U */ + 300 300 300 300 300 /* CG,GU,N,N */ + 300 300 300 300 300 /* CG,GU,N,A */ + 300 300 300 300 300 /* CG,GU,N,C */ + 300 300 300 300 300 /* CG,GU,N,G */ + 300 300 300 300 300 /* CG,GU,N,U */ + 300 300 300 190 300 /* CG,GU,A,N */ + 300 300 300 190 300 /* CG,GU,A,A */ + 300 300 300 190 300 /* CG,GU,A,C */ + 190 190 190 190 190 /* CG,GU,A,G */ + 300 300 300 190 300 /* CG,GU,A,U */ + 300 300 300 300 300 /* CG,GU,C,N */ + 300 300 300 300 300 /* CG,GU,C,A */ + 300 300 300 300 300 /* CG,GU,C,C */ + 300 300 300 300 300 /* CG,GU,C,G */ + 300 300 300 300 300 /* CG,GU,C,U */ + 300 190 300 190 300 /* CG,GU,G,N */ + 300 190 300 190 300 /* CG,GU,G,A */ + 300 190 300 190 300 /* CG,GU,G,C */ + 190 190 190 190 190 /* CG,GU,G,G */ + 300 190 300 190 300 /* CG,GU,G,U */ + 300 300 300 300 220 /* CG,GU,U,N */ + 300 300 300 300 220 /* CG,GU,U,A */ + 300 300 300 300 220 /* CG,GU,U,C */ + 300 300 300 300 220 /* CG,GU,U,G */ + 220 220 220 220 220 /* CG,GU,U,U */ + 300 300 300 300 300 /* CG,UG,N,N */ + 300 300 300 300 300 /* CG,UG,N,A */ + 300 300 300 300 300 /* CG,UG,N,C */ + 300 300 300 300 300 /* CG,UG,N,G */ + 300 300 300 300 300 /* CG,UG,N,U */ + 300 300 300 190 300 /* CG,UG,A,N */ + 300 300 300 190 300 /* CG,UG,A,A */ + 300 300 300 190 300 /* CG,UG,A,C */ + 190 190 190 190 190 /* CG,UG,A,G */ + 300 300 300 190 300 /* CG,UG,A,U */ + 300 300 300 300 300 /* CG,UG,C,N */ + 300 300 300 300 300 /* CG,UG,C,A */ + 300 300 300 300 300 /* CG,UG,C,C */ + 300 300 300 300 300 /* CG,UG,C,G */ + 300 300 300 300 300 /* CG,UG,C,U */ + 300 190 300 190 300 /* CG,UG,G,N */ + 190 190 190 190 190 /* CG,UG,G,A */ + 300 190 300 190 300 /* CG,UG,G,C */ + 190 190 190 190 190 /* CG,UG,G,G */ + 300 190 300 190 300 /* CG,UG,G,U */ + 300 300 300 300 220 /* CG,UG,U,N */ + 300 300 300 300 220 /* CG,UG,U,A */ + 300 300 300 300 220 /* CG,UG,U,C */ + 300 300 300 300 220 /* CG,UG,U,G */ + 220 220 220 220 220 /* CG,UG,U,U */ + 300 300 300 300 300 /* CG,AU,N,N */ + 300 300 300 300 300 /* CG,AU,N,A */ + 300 300 300 300 300 /* CG,AU,N,C */ + 300 300 300 300 300 /* CG,AU,N,G */ + 300 300 300 300 300 /* CG,AU,N,U */ + 300 300 300 190 300 /* CG,AU,A,N */ + 300 300 300 190 300 /* CG,AU,A,A */ + 300 300 300 190 300 /* CG,AU,A,C */ + 190 190 190 190 190 /* CG,AU,A,G */ + 300 300 300 190 300 /* CG,AU,A,U */ + 300 300 300 300 300 /* CG,AU,C,N */ + 300 300 300 300 300 /* CG,AU,C,A */ + 300 300 300 300 300 /* CG,AU,C,C */ + 300 300 300 300 300 /* CG,AU,C,G */ + 300 300 300 300 300 /* CG,AU,C,U */ + 300 190 300 190 300 /* CG,AU,G,N */ + 300 190 300 190 300 /* CG,AU,G,A */ + 300 190 300 190 300 /* CG,AU,G,C */ + 190 190 190 190 190 /* CG,AU,G,G */ + 300 190 300 190 300 /* CG,AU,G,U */ + 300 300 300 300 220 /* CG,AU,U,N */ + 300 300 300 300 220 /* CG,AU,U,A */ + 300 300 300 300 220 /* CG,AU,U,C */ + 300 300 300 300 220 /* CG,AU,U,G */ + 220 220 220 220 220 /* CG,AU,U,U */ + 300 300 300 300 300 /* CG,UA,N,N */ + 300 300 300 300 300 /* CG,UA,N,A */ + 300 300 300 300 300 /* CG,UA,N,C */ + 300 300 300 300 300 /* CG,UA,N,G */ + 300 300 300 300 300 /* CG,UA,N,U */ + 300 300 300 190 300 /* CG,UA,A,N */ + 300 300 300 190 300 /* CG,UA,A,A */ + 300 300 300 190 300 /* CG,UA,A,C */ + 190 190 190 190 190 /* CG,UA,A,G */ + 300 300 300 190 300 /* CG,UA,A,U */ + 300 300 300 300 300 /* CG,UA,C,N */ + 300 300 300 300 300 /* CG,UA,C,A */ + 300 300 300 300 300 /* CG,UA,C,C */ + 300 300 300 300 300 /* CG,UA,C,G */ + 300 300 300 300 300 /* CG,UA,C,U */ + 300 190 300 190 300 /* CG,UA,G,N */ + 190 190 190 190 190 /* CG,UA,G,A */ + 300 190 300 190 300 /* CG,UA,G,C */ + 190 190 190 190 190 /* CG,UA,G,G */ + 300 190 300 190 300 /* CG,UA,G,U */ + 300 300 300 300 220 /* CG,UA,U,N */ + 300 300 300 300 220 /* CG,UA,U,A */ + 300 300 300 300 220 /* CG,UA,U,C */ + 300 300 300 300 220 /* CG,UA,U,G */ + 220 220 220 220 220 /* CG,UA,U,U */ + 300 300 300 300 300 /* CG,NN,N,N */ + 300 300 300 300 300 /* CG,NN,N,A */ + 300 300 300 300 300 /* CG,NN,N,C */ + 300 300 300 300 300 /* CG,NN,N,G */ + 300 300 300 300 300 /* CG,NN,N,U */ + 300 300 300 190 300 /* CG,NN,A,N */ + 300 300 300 190 300 /* CG,NN,A,A */ + 300 300 300 190 300 /* CG,NN,A,C */ + 190 190 190 190 190 /* CG,NN,A,G */ + 300 300 300 190 300 /* CG,NN,A,U */ + 300 300 300 300 300 /* CG,NN,C,N */ + 300 300 300 300 300 /* CG,NN,C,A */ + 300 300 300 300 300 /* CG,NN,C,C */ + 300 300 300 300 300 /* CG,NN,C,G */ + 300 300 300 300 300 /* CG,NN,C,U */ + 300 190 300 190 300 /* CG,NN,G,N */ + 300 190 300 190 300 /* CG,NN,G,A */ + 300 190 300 190 300 /* CG,NN,G,C */ + 190 190 190 190 190 /* CG,NN,G,G */ + 300 190 300 190 300 /* CG,NN,G,U */ + 300 300 300 300 220 /* CG,NN,U,N */ + 300 300 300 300 220 /* CG,NN,U,A */ + 300 300 300 300 220 /* CG,NN,U,C */ + 300 300 300 300 220 /* CG,NN,U,G */ + 220 220 220 220 220 /* CG,NN,U,U */ + 250 250 230 230 230 /* GC,CG,N,N */ + 250 250 230 230 230 /* GC,CG,N,A */ + 230 230 230 230 230 /* GC,CG,N,C */ + 230 230 230 230 230 /* GC,CG,N,G */ + 230 230 230 230 230 /* GC,CG,N,U */ + 250 250 230 230 230 /* GC,CG,A,N */ + 250 250 230 210 230 /* GC,CG,A,A */ + 230 230 230 230 230 /* GC,CG,A,C */ + 120 120 110 110 110 /* GC,CG,A,G */ + 230 230 230 230 230 /* GC,CG,A,U */ + 230 230 230 230 230 /* GC,CG,C,N */ + 230 230 230 230 230 /* GC,CG,C,A */ + 230 230 230 230 230 /* GC,CG,C,C */ + 230 230 230 230 230 /* GC,CG,C,G */ + 230 230 190 230 230 /* GC,CG,C,U */ + 230 110 230 110 230 /* GC,CG,G,N */ + 110 110 110 110 110 /* GC,CG,G,A */ + 230 110 230 110 230 /* GC,CG,G,C */ + 110 110 110 110 110 /* GC,CG,G,G */ + 230 110 230 110 230 /* GC,CG,G,U */ + 230 230 230 230 150 /* GC,CG,U,N */ + 230 230 230 230 150 /* GC,CG,U,A */ + 230 230 230 230 150 /* GC,CG,U,C */ + 230 230 230 230 150 /* GC,CG,U,G */ + 150 150 150 150 150 /* GC,CG,U,U */ + 230 230 230 230 230 /* GC,GC,N,N */ + 230 230 230 230 230 /* GC,GC,N,A */ + 230 230 230 230 230 /* GC,GC,N,C */ + 230 230 230 230 230 /* GC,GC,N,G */ + 230 230 230 230 230 /* GC,GC,N,U */ + 230 230 230 230 230 /* GC,GC,A,N */ + 230 230 230 230 230 /* GC,GC,A,A */ + 230 230 230 230 230 /* GC,GC,A,C */ + 110 110 110 110 110 /* GC,GC,A,G */ + 230 230 230 230 230 /* GC,GC,A,U */ + 230 230 230 230 230 /* GC,GC,C,N */ + 230 230 230 230 230 /* GC,GC,C,A */ + 230 230 230 230 230 /* GC,GC,C,C */ + 230 230 230 230 230 /* GC,GC,C,G */ + 230 230 230 230 230 /* GC,GC,C,U */ + 230 110 230 110 230 /* GC,GC,G,N */ + 230 110 230 110 230 /* GC,GC,G,A */ + 230 110 230 110 230 /* GC,GC,G,C */ + 110 110 110 110 110 /* GC,GC,G,G */ + 230 110 230 110 230 /* GC,GC,G,U */ + 230 230 230 230 150 /* GC,GC,U,N */ + 230 230 230 230 150 /* GC,GC,U,A */ + 230 230 230 230 150 /* GC,GC,U,C */ + 230 230 230 230 150 /* GC,GC,U,G */ + 150 150 150 150 150 /* GC,GC,U,U */ + 300 300 300 300 300 /* GC,GU,N,N */ + 300 300 300 300 300 /* GC,GU,N,A */ + 300 300 300 300 300 /* GC,GU,N,C */ + 300 300 300 300 300 /* GC,GU,N,G */ + 300 300 300 300 300 /* GC,GU,N,U */ + 300 300 300 300 300 /* GC,GU,A,N */ + 300 300 300 300 300 /* GC,GU,A,A */ + 300 300 300 300 300 /* GC,GU,A,C */ + 190 190 190 190 190 /* GC,GU,A,G */ + 300 300 300 300 300 /* GC,GU,A,U */ + 300 300 300 300 300 /* GC,GU,C,N */ + 300 300 300 300 300 /* GC,GU,C,A */ + 300 300 300 300 300 /* GC,GU,C,C */ + 300 300 300 300 300 /* GC,GU,C,G */ + 300 300 300 300 300 /* GC,GU,C,U */ + 300 190 300 190 300 /* GC,GU,G,N */ + 300 190 300 190 300 /* GC,GU,G,A */ + 300 190 300 190 300 /* GC,GU,G,C */ + 190 190 190 190 190 /* GC,GU,G,G */ + 300 190 300 190 300 /* GC,GU,G,U */ + 300 300 300 300 220 /* GC,GU,U,N */ + 300 300 300 300 220 /* GC,GU,U,A */ + 300 300 300 300 220 /* GC,GU,U,C */ + 300 300 300 300 220 /* GC,GU,U,G */ + 220 220 220 220 220 /* GC,GU,U,U */ + 300 300 300 300 300 /* GC,UG,N,N */ + 300 300 300 300 300 /* GC,UG,N,A */ + 300 300 300 300 300 /* GC,UG,N,C */ + 300 300 300 300 300 /* GC,UG,N,G */ + 300 300 300 300 300 /* GC,UG,N,U */ + 300 300 300 300 300 /* GC,UG,A,N */ + 300 250 300 210 300 /* GC,UG,A,A */ + 300 300 300 300 300 /* GC,UG,A,C */ + 190 120 190 190 190 /* GC,UG,A,G */ + 300 300 300 300 300 /* GC,UG,A,U */ + 300 300 300 300 300 /* GC,UG,C,N */ + 300 300 300 300 300 /* GC,UG,C,A */ + 300 300 300 300 300 /* GC,UG,C,C */ + 300 300 300 300 300 /* GC,UG,C,G */ + 300 300 190 300 300 /* GC,UG,C,U */ + 300 190 300 190 300 /* GC,UG,G,N */ + 190 190 190 190 190 /* GC,UG,G,A */ + 300 190 300 190 300 /* GC,UG,G,C */ + 190 190 190 190 190 /* GC,UG,G,G */ + 300 190 300 190 300 /* GC,UG,G,U */ + 300 300 300 300 220 /* GC,UG,U,N */ + 300 300 300 300 220 /* GC,UG,U,A */ + 300 300 300 300 220 /* GC,UG,U,C */ + 300 300 300 300 220 /* GC,UG,U,G */ + 220 220 220 220 220 /* GC,UG,U,U */ + 300 300 300 300 300 /* GC,AU,N,N */ + 300 300 300 300 300 /* GC,AU,N,A */ + 300 300 300 300 300 /* GC,AU,N,C */ + 300 300 300 300 300 /* GC,AU,N,G */ + 300 300 300 300 300 /* GC,AU,N,U */ + 300 300 300 300 300 /* GC,AU,A,N */ + 300 300 300 300 300 /* GC,AU,A,A */ + 300 300 300 300 300 /* GC,AU,A,C */ + 190 190 190 190 190 /* GC,AU,A,G */ + 300 300 300 300 300 /* GC,AU,A,U */ + 300 300 300 300 300 /* GC,AU,C,N */ + 300 300 300 300 300 /* GC,AU,C,A */ + 300 300 300 300 300 /* GC,AU,C,C */ + 300 300 300 300 300 /* GC,AU,C,G */ + 300 300 300 300 300 /* GC,AU,C,U */ + 300 190 300 190 300 /* GC,AU,G,N */ + 300 190 300 190 300 /* GC,AU,G,A */ + 300 190 300 190 300 /* GC,AU,G,C */ + 190 190 190 190 190 /* GC,AU,G,G */ + 300 190 300 190 300 /* GC,AU,G,U */ + 300 300 300 300 220 /* GC,AU,U,N */ + 300 300 300 300 220 /* GC,AU,U,A */ + 300 300 300 300 220 /* GC,AU,U,C */ + 300 300 300 300 220 /* GC,AU,U,G */ + 220 220 220 220 220 /* GC,AU,U,U */ + 300 300 300 300 300 /* GC,UA,N,N */ + 300 300 300 300 300 /* GC,UA,N,A */ + 300 300 300 300 300 /* GC,UA,N,C */ + 300 300 300 300 300 /* GC,UA,N,G */ + 300 300 300 300 300 /* GC,UA,N,U */ + 300 300 300 300 300 /* GC,UA,A,N */ + 300 300 300 300 300 /* GC,UA,A,A */ + 300 300 300 300 300 /* GC,UA,A,C */ + 190 190 190 190 190 /* GC,UA,A,G */ + 300 300 300 300 300 /* GC,UA,A,U */ + 300 300 300 300 300 /* GC,UA,C,N */ + 300 300 300 300 300 /* GC,UA,C,A */ + 300 300 300 300 300 /* GC,UA,C,C */ + 300 300 300 300 300 /* GC,UA,C,G */ + 300 300 300 300 300 /* GC,UA,C,U */ + 300 190 300 190 300 /* GC,UA,G,N */ + 190 190 190 190 190 /* GC,UA,G,A */ + 300 190 300 190 300 /* GC,UA,G,C */ + 190 190 190 190 190 /* GC,UA,G,G */ + 300 190 300 190 300 /* GC,UA,G,U */ + 300 300 300 300 220 /* GC,UA,U,N */ + 300 300 300 300 220 /* GC,UA,U,A */ + 300 300 300 300 220 /* GC,UA,U,C */ + 300 300 300 300 220 /* GC,UA,U,G */ + 220 220 220 220 220 /* GC,UA,U,U */ + 300 300 300 300 300 /* GC,NN,N,N */ + 300 300 300 300 300 /* GC,NN,N,A */ + 300 300 300 300 300 /* GC,NN,N,C */ + 300 300 300 300 300 /* GC,NN,N,G */ + 300 300 300 300 300 /* GC,NN,N,U */ + 300 300 300 300 300 /* GC,NN,A,N */ + 300 300 300 300 300 /* GC,NN,A,A */ + 300 300 300 300 300 /* GC,NN,A,C */ + 190 190 190 190 190 /* GC,NN,A,G */ + 300 300 300 300 300 /* GC,NN,A,U */ + 300 300 300 300 300 /* GC,NN,C,N */ + 300 300 300 300 300 /* GC,NN,C,A */ + 300 300 300 300 300 /* GC,NN,C,C */ + 300 300 300 300 300 /* GC,NN,C,G */ + 300 300 300 300 300 /* GC,NN,C,U */ + 300 190 300 190 300 /* GC,NN,G,N */ + 300 190 300 190 300 /* GC,NN,G,A */ + 300 190 300 190 300 /* GC,NN,G,C */ + 190 190 190 190 190 /* GC,NN,G,G */ + 300 190 300 190 300 /* GC,NN,G,U */ + 300 300 300 300 220 /* GC,NN,U,N */ + 300 300 300 300 220 /* GC,NN,U,A */ + 300 300 300 300 220 /* GC,NN,U,C */ + 300 300 300 300 220 /* GC,NN,U,G */ + 220 220 220 220 220 /* GC,NN,U,U */ + 300 300 300 300 300 /* GU,CG,N,N */ + 300 300 300 300 300 /* GU,CG,N,A */ + 300 300 300 300 300 /* GU,CG,N,C */ + 300 300 300 300 300 /* GU,CG,N,G */ + 300 300 300 300 300 /* GU,CG,N,U */ + 300 300 300 300 300 /* GU,CG,A,N */ + 300 250 300 210 300 /* GU,CG,A,A */ + 300 300 300 300 300 /* GU,CG,A,C */ + 190 120 190 190 190 /* GU,CG,A,G */ + 300 300 300 300 300 /* GU,CG,A,U */ + 300 300 300 300 300 /* GU,CG,C,N */ + 300 300 300 300 300 /* GU,CG,C,A */ + 300 300 300 300 300 /* GU,CG,C,C */ + 300 300 300 300 300 /* GU,CG,C,G */ + 300 300 190 300 300 /* GU,CG,C,U */ + 300 190 300 190 300 /* GU,CG,G,N */ + 190 190 190 190 190 /* GU,CG,G,A */ + 300 190 300 190 300 /* GU,CG,G,C */ + 190 190 190 190 190 /* GU,CG,G,G */ + 300 190 300 190 300 /* GU,CG,G,U */ + 300 300 300 300 220 /* GU,CG,U,N */ + 300 300 300 300 220 /* GU,CG,U,A */ + 300 300 300 300 220 /* GU,CG,U,C */ + 300 300 300 300 220 /* GU,CG,U,G */ + 220 220 220 220 220 /* GU,CG,U,U */ + 300 300 300 300 300 /* GU,GC,N,N */ + 300 300 300 300 300 /* GU,GC,N,A */ + 300 300 300 300 300 /* GU,GC,N,C */ + 300 300 300 300 300 /* GU,GC,N,G */ + 300 300 300 300 300 /* GU,GC,N,U */ + 300 300 300 300 300 /* GU,GC,A,N */ + 300 300 300 300 300 /* GU,GC,A,A */ + 300 300 300 300 300 /* GU,GC,A,C */ + 190 190 190 190 190 /* GU,GC,A,G */ + 300 300 300 300 300 /* GU,GC,A,U */ + 300 300 300 300 300 /* GU,GC,C,N */ + 300 300 300 300 300 /* GU,GC,C,A */ + 300 300 300 300 300 /* GU,GC,C,C */ + 300 300 300 300 300 /* GU,GC,C,G */ + 300 300 300 300 300 /* GU,GC,C,U */ + 300 190 300 190 300 /* GU,GC,G,N */ + 300 190 300 190 300 /* GU,GC,G,A */ + 300 190 300 190 300 /* GU,GC,G,C */ + 190 190 190 190 190 /* GU,GC,G,G */ + 300 190 300 190 300 /* GU,GC,G,U */ + 300 300 300 300 220 /* GU,GC,U,N */ + 300 300 300 300 220 /* GU,GC,U,A */ + 300 300 300 300 220 /* GU,GC,U,C */ + 300 300 300 300 220 /* GU,GC,U,G */ + 220 220 220 220 220 /* GU,GC,U,U */ + 370 370 370 370 370 /* GU,GU,N,N */ + 370 370 370 370 370 /* GU,GU,N,A */ + 370 370 370 370 370 /* GU,GU,N,C */ + 370 370 370 370 370 /* GU,GU,N,G */ + 370 370 370 370 370 /* GU,GU,N,U */ + 370 370 370 370 370 /* GU,GU,A,N */ + 370 370 370 370 370 /* GU,GU,A,A */ + 370 370 370 370 370 /* GU,GU,A,C */ + 260 260 260 260 260 /* GU,GU,A,G */ + 370 370 370 370 370 /* GU,GU,A,U */ + 370 370 370 370 370 /* GU,GU,C,N */ + 370 370 370 370 370 /* GU,GU,C,A */ + 370 370 370 370 370 /* GU,GU,C,C */ + 370 370 370 370 370 /* GU,GU,C,G */ + 370 370 370 370 370 /* GU,GU,C,U */ + 370 260 370 260 370 /* GU,GU,G,N */ + 370 260 370 260 370 /* GU,GU,G,A */ + 370 260 370 260 370 /* GU,GU,G,C */ + 260 260 260 260 260 /* GU,GU,G,G */ + 370 260 370 260 370 /* GU,GU,G,U */ + 370 370 370 370 300 /* GU,GU,U,N */ + 370 370 370 370 300 /* GU,GU,U,A */ + 370 370 370 370 300 /* GU,GU,U,C */ + 370 370 370 370 300 /* GU,GU,U,G */ + 300 300 300 300 300 /* GU,GU,U,U */ + 370 370 370 370 370 /* GU,UG,N,N */ + 370 370 370 370 370 /* GU,UG,N,A */ + 370 370 370 370 370 /* GU,UG,N,C */ + 370 370 370 370 370 /* GU,UG,N,G */ + 370 370 370 370 370 /* GU,UG,N,U */ + 370 370 370 370 370 /* GU,UG,A,N */ + 370 250 370 210 370 /* GU,UG,A,A */ + 370 370 370 370 370 /* GU,UG,A,C */ + 260 120 260 260 260 /* GU,UG,A,G */ + 370 370 370 370 370 /* GU,UG,A,U */ + 370 370 370 370 370 /* GU,UG,C,N */ + 370 370 370 370 370 /* GU,UG,C,A */ + 370 370 370 370 370 /* GU,UG,C,C */ + 370 370 370 370 370 /* GU,UG,C,G */ + 370 370 190 370 370 /* GU,UG,C,U */ + 370 260 370 260 370 /* GU,UG,G,N */ + 260 260 260 260 260 /* GU,UG,G,A */ + 370 260 370 260 370 /* GU,UG,G,C */ + 260 260 260 260 260 /* GU,UG,G,G */ + 370 260 370 260 370 /* GU,UG,G,U */ + 370 370 370 370 300 /* GU,UG,U,N */ + 370 370 370 370 300 /* GU,UG,U,A */ + 370 370 370 370 300 /* GU,UG,U,C */ + 370 370 370 370 300 /* GU,UG,U,G */ + 300 300 300 300 300 /* GU,UG,U,U */ + 370 370 370 370 370 /* GU,AU,N,N */ + 370 370 370 370 370 /* GU,AU,N,A */ + 370 370 370 370 370 /* GU,AU,N,C */ + 370 370 370 370 370 /* GU,AU,N,G */ + 370 370 370 370 370 /* GU,AU,N,U */ + 370 370 370 370 370 /* GU,AU,A,N */ + 370 370 370 370 370 /* GU,AU,A,A */ + 370 370 370 370 370 /* GU,AU,A,C */ + 260 260 260 260 260 /* GU,AU,A,G */ + 370 370 370 370 370 /* GU,AU,A,U */ + 370 370 370 370 370 /* GU,AU,C,N */ + 370 370 370 370 370 /* GU,AU,C,A */ + 370 370 370 370 370 /* GU,AU,C,C */ + 370 370 370 370 370 /* GU,AU,C,G */ + 370 370 370 370 370 /* GU,AU,C,U */ + 370 260 370 260 370 /* GU,AU,G,N */ + 370 260 370 260 370 /* GU,AU,G,A */ + 370 260 370 260 370 /* GU,AU,G,C */ + 260 260 260 260 260 /* GU,AU,G,G */ + 370 260 370 260 370 /* GU,AU,G,U */ + 370 370 370 370 300 /* GU,AU,U,N */ + 370 370 370 370 300 /* GU,AU,U,A */ + 370 370 370 370 300 /* GU,AU,U,C */ + 370 370 370 370 300 /* GU,AU,U,G */ + 300 300 300 300 300 /* GU,AU,U,U */ + 370 370 370 370 370 /* GU,UA,N,N */ + 370 370 370 370 370 /* GU,UA,N,A */ + 370 370 370 370 370 /* GU,UA,N,C */ + 370 370 370 370 370 /* GU,UA,N,G */ + 370 370 370 370 370 /* GU,UA,N,U */ + 370 370 370 370 370 /* GU,UA,A,N */ + 370 370 370 370 370 /* GU,UA,A,A */ + 370 370 370 370 370 /* GU,UA,A,C */ + 260 260 260 260 260 /* GU,UA,A,G */ + 370 370 370 370 370 /* GU,UA,A,U */ + 370 370 370 370 370 /* GU,UA,C,N */ + 370 370 370 370 370 /* GU,UA,C,A */ + 370 370 370 370 370 /* GU,UA,C,C */ + 370 370 370 370 370 /* GU,UA,C,G */ + 370 370 370 370 370 /* GU,UA,C,U */ + 370 260 370 260 370 /* GU,UA,G,N */ + 260 260 260 260 260 /* GU,UA,G,A */ + 370 260 370 260 370 /* GU,UA,G,C */ + 260 260 260 260 260 /* GU,UA,G,G */ + 370 260 370 260 370 /* GU,UA,G,U */ + 370 370 370 370 300 /* GU,UA,U,N */ + 370 370 370 370 300 /* GU,UA,U,A */ + 370 370 370 370 300 /* GU,UA,U,C */ + 370 370 370 370 300 /* GU,UA,U,G */ + 300 300 300 300 300 /* GU,UA,U,U */ + 370 370 370 370 370 /* GU,NN,N,N */ + 370 370 370 370 370 /* GU,NN,N,A */ + 370 370 370 370 370 /* GU,NN,N,C */ + 370 370 370 370 370 /* GU,NN,N,G */ + 370 370 370 370 370 /* GU,NN,N,U */ + 370 370 370 370 370 /* GU,NN,A,N */ + 370 370 370 370 370 /* GU,NN,A,A */ + 370 370 370 370 370 /* GU,NN,A,C */ + 260 260 260 260 260 /* GU,NN,A,G */ + 370 370 370 370 370 /* GU,NN,A,U */ + 370 370 370 370 370 /* GU,NN,C,N */ + 370 370 370 370 370 /* GU,NN,C,A */ + 370 370 370 370 370 /* GU,NN,C,C */ + 370 370 370 370 370 /* GU,NN,C,G */ + 370 370 370 370 370 /* GU,NN,C,U */ + 370 260 370 260 370 /* GU,NN,G,N */ + 370 260 370 260 370 /* GU,NN,G,A */ + 370 260 370 260 370 /* GU,NN,G,C */ + 260 260 260 260 260 /* GU,NN,G,G */ + 370 260 370 260 370 /* GU,NN,G,U */ + 370 370 370 370 300 /* GU,NN,U,N */ + 370 370 370 370 300 /* GU,NN,U,A */ + 370 370 370 370 300 /* GU,NN,U,C */ + 370 370 370 370 300 /* GU,NN,U,G */ + 300 300 300 300 300 /* GU,NN,U,U */ + 300 300 300 300 300 /* UG,CG,N,N */ + 300 300 300 300 300 /* UG,CG,N,A */ + 300 300 300 300 300 /* UG,CG,N,C */ + 300 300 300 300 300 /* UG,CG,N,G */ + 300 300 300 300 300 /* UG,CG,N,U */ + 300 300 300 190 300 /* UG,CG,A,N */ + 300 300 300 190 300 /* UG,CG,A,A */ + 300 300 300 190 300 /* UG,CG,A,C */ + 190 190 190 190 190 /* UG,CG,A,G */ + 300 300 300 190 300 /* UG,CG,A,U */ + 300 300 300 300 300 /* UG,CG,C,N */ + 300 300 300 300 300 /* UG,CG,C,A */ + 300 300 300 300 300 /* UG,CG,C,C */ + 300 300 300 300 300 /* UG,CG,C,G */ + 300 300 300 300 300 /* UG,CG,C,U */ + 300 190 300 190 300 /* UG,CG,G,N */ + 190 190 190 190 190 /* UG,CG,G,A */ + 300 190 300 190 300 /* UG,CG,G,C */ + 190 190 190 190 190 /* UG,CG,G,G */ + 300 190 300 190 300 /* UG,CG,G,U */ + 300 300 300 300 220 /* UG,CG,U,N */ + 300 300 300 300 220 /* UG,CG,U,A */ + 300 300 300 300 220 /* UG,CG,U,C */ + 300 300 300 300 220 /* UG,CG,U,G */ + 220 220 220 220 220 /* UG,CG,U,U */ + 300 300 300 300 300 /* UG,GC,N,N */ + 300 300 300 300 300 /* UG,GC,N,A */ + 300 300 300 300 300 /* UG,GC,N,C */ + 300 300 300 300 300 /* UG,GC,N,G */ + 300 300 300 300 300 /* UG,GC,N,U */ + 300 300 300 190 300 /* UG,GC,A,N */ + 300 300 300 190 300 /* UG,GC,A,A */ + 300 300 300 190 300 /* UG,GC,A,C */ + 190 190 190 190 190 /* UG,GC,A,G */ + 300 300 300 190 300 /* UG,GC,A,U */ + 300 300 300 300 300 /* UG,GC,C,N */ + 300 300 300 300 300 /* UG,GC,C,A */ + 300 300 300 300 300 /* UG,GC,C,C */ + 300 300 300 300 300 /* UG,GC,C,G */ + 300 300 300 300 300 /* UG,GC,C,U */ + 300 190 300 190 300 /* UG,GC,G,N */ + 300 190 300 190 300 /* UG,GC,G,A */ + 300 190 300 190 300 /* UG,GC,G,C */ + 190 190 190 190 190 /* UG,GC,G,G */ + 300 190 300 190 300 /* UG,GC,G,U */ + 300 300 300 300 220 /* UG,GC,U,N */ + 300 300 300 300 220 /* UG,GC,U,A */ + 300 300 300 300 220 /* UG,GC,U,C */ + 300 300 300 300 220 /* UG,GC,U,G */ + 220 220 220 220 220 /* UG,GC,U,U */ + 370 370 370 370 370 /* UG,GU,N,N */ + 370 370 370 370 370 /* UG,GU,N,A */ + 370 370 370 370 370 /* UG,GU,N,C */ + 370 370 370 370 370 /* UG,GU,N,G */ + 370 370 370 370 370 /* UG,GU,N,U */ + 370 370 370 260 370 /* UG,GU,A,N */ + 370 370 370 260 370 /* UG,GU,A,A */ + 370 370 370 260 370 /* UG,GU,A,C */ + 260 260 260 260 260 /* UG,GU,A,G */ + 370 370 370 260 370 /* UG,GU,A,U */ + 370 370 370 370 370 /* UG,GU,C,N */ + 370 370 370 370 370 /* UG,GU,C,A */ + 370 370 370 370 370 /* UG,GU,C,C */ + 370 370 370 370 370 /* UG,GU,C,G */ + 370 370 370 370 370 /* UG,GU,C,U */ + 370 260 370 260 370 /* UG,GU,G,N */ + 370 260 370 260 370 /* UG,GU,G,A */ + 370 260 370 260 370 /* UG,GU,G,C */ + 260 260 260 260 260 /* UG,GU,G,G */ + 370 260 370 260 370 /* UG,GU,G,U */ + 370 370 370 370 300 /* UG,GU,U,N */ + 370 370 370 370 300 /* UG,GU,U,A */ + 370 370 370 370 300 /* UG,GU,U,C */ + 370 370 370 370 300 /* UG,GU,U,G */ + 300 300 300 300 300 /* UG,GU,U,U */ + 370 370 370 370 370 /* UG,UG,N,N */ + 370 370 370 370 370 /* UG,UG,N,A */ + 370 370 370 370 370 /* UG,UG,N,C */ + 370 370 370 370 370 /* UG,UG,N,G */ + 370 370 370 370 370 /* UG,UG,N,U */ + 370 370 370 260 370 /* UG,UG,A,N */ + 370 370 370 260 370 /* UG,UG,A,A */ + 370 370 370 260 370 /* UG,UG,A,C */ + 260 260 260 260 260 /* UG,UG,A,G */ + 370 370 370 260 370 /* UG,UG,A,U */ + 370 370 370 370 370 /* UG,UG,C,N */ + 370 370 370 370 370 /* UG,UG,C,A */ + 370 370 370 370 370 /* UG,UG,C,C */ + 370 370 370 370 370 /* UG,UG,C,G */ + 370 370 370 370 370 /* UG,UG,C,U */ + 370 260 370 260 370 /* UG,UG,G,N */ + 260 260 260 260 260 /* UG,UG,G,A */ + 370 260 370 260 370 /* UG,UG,G,C */ + 260 260 260 260 260 /* UG,UG,G,G */ + 370 260 370 260 370 /* UG,UG,G,U */ + 370 370 370 370 300 /* UG,UG,U,N */ + 370 370 370 370 300 /* UG,UG,U,A */ + 370 370 370 370 300 /* UG,UG,U,C */ + 370 370 370 370 300 /* UG,UG,U,G */ + 300 300 300 300 300 /* UG,UG,U,U */ + 370 370 370 370 370 /* UG,AU,N,N */ + 370 370 370 370 370 /* UG,AU,N,A */ + 370 370 370 370 370 /* UG,AU,N,C */ + 370 370 370 370 370 /* UG,AU,N,G */ + 370 370 370 370 370 /* UG,AU,N,U */ + 370 370 370 260 370 /* UG,AU,A,N */ + 370 370 370 260 370 /* UG,AU,A,A */ + 370 370 370 260 370 /* UG,AU,A,C */ + 260 260 260 260 260 /* UG,AU,A,G */ + 370 370 370 260 370 /* UG,AU,A,U */ + 370 370 370 370 370 /* UG,AU,C,N */ + 370 370 370 370 370 /* UG,AU,C,A */ + 370 370 370 370 370 /* UG,AU,C,C */ + 370 370 370 370 370 /* UG,AU,C,G */ + 370 370 370 370 370 /* UG,AU,C,U */ + 370 260 370 260 370 /* UG,AU,G,N */ + 370 260 370 260 370 /* UG,AU,G,A */ + 370 260 370 260 370 /* UG,AU,G,C */ + 260 260 260 260 260 /* UG,AU,G,G */ + 370 260 370 260 370 /* UG,AU,G,U */ + 370 370 370 370 300 /* UG,AU,U,N */ + 370 370 370 370 300 /* UG,AU,U,A */ + 370 370 370 370 300 /* UG,AU,U,C */ + 370 370 370 370 300 /* UG,AU,U,G */ + 300 300 300 300 300 /* UG,AU,U,U */ + 370 370 370 370 370 /* UG,UA,N,N */ + 370 370 370 370 370 /* UG,UA,N,A */ + 370 370 370 370 370 /* UG,UA,N,C */ + 370 370 370 370 370 /* UG,UA,N,G */ + 370 370 370 370 370 /* UG,UA,N,U */ + 370 370 370 260 370 /* UG,UA,A,N */ + 370 370 370 260 370 /* UG,UA,A,A */ + 370 370 370 260 370 /* UG,UA,A,C */ + 260 260 260 260 260 /* UG,UA,A,G */ + 370 370 370 260 370 /* UG,UA,A,U */ + 370 370 370 370 370 /* UG,UA,C,N */ + 370 370 370 370 370 /* UG,UA,C,A */ + 370 370 370 370 370 /* UG,UA,C,C */ + 370 370 370 370 370 /* UG,UA,C,G */ + 370 370 370 370 370 /* UG,UA,C,U */ + 370 260 370 260 370 /* UG,UA,G,N */ + 260 260 260 260 260 /* UG,UA,G,A */ + 370 260 370 260 370 /* UG,UA,G,C */ + 260 260 260 260 260 /* UG,UA,G,G */ + 370 260 370 260 370 /* UG,UA,G,U */ + 370 370 370 370 300 /* UG,UA,U,N */ + 370 370 370 370 300 /* UG,UA,U,A */ + 370 370 370 370 300 /* UG,UA,U,C */ + 370 370 370 370 300 /* UG,UA,U,G */ + 300 300 300 300 300 /* UG,UA,U,U */ + 370 370 370 370 370 /* UG,NN,N,N */ + 370 370 370 370 370 /* UG,NN,N,A */ + 370 370 370 370 370 /* UG,NN,N,C */ + 370 370 370 370 370 /* UG,NN,N,G */ + 370 370 370 370 370 /* UG,NN,N,U */ + 370 370 370 260 370 /* UG,NN,A,N */ + 370 370 370 260 370 /* UG,NN,A,A */ + 370 370 370 260 370 /* UG,NN,A,C */ + 260 260 260 260 260 /* UG,NN,A,G */ + 370 370 370 260 370 /* UG,NN,A,U */ + 370 370 370 370 370 /* UG,NN,C,N */ + 370 370 370 370 370 /* UG,NN,C,A */ + 370 370 370 370 370 /* UG,NN,C,C */ + 370 370 370 370 370 /* UG,NN,C,G */ + 370 370 370 370 370 /* UG,NN,C,U */ + 370 260 370 260 370 /* UG,NN,G,N */ + 370 260 370 260 370 /* UG,NN,G,A */ + 370 260 370 260 370 /* UG,NN,G,C */ + 260 260 260 260 260 /* UG,NN,G,G */ + 370 260 370 260 370 /* UG,NN,G,U */ + 370 370 370 370 300 /* UG,NN,U,N */ + 370 370 370 370 300 /* UG,NN,U,A */ + 370 370 370 370 300 /* UG,NN,U,C */ + 370 370 370 370 300 /* UG,NN,U,G */ + 300 300 300 300 300 /* UG,NN,U,U */ + 300 300 300 300 300 /* AU,CG,N,N */ + 300 300 300 300 300 /* AU,CG,N,A */ + 300 300 300 300 300 /* AU,CG,N,C */ + 300 300 300 300 300 /* AU,CG,N,G */ + 300 300 300 300 300 /* AU,CG,N,U */ + 300 300 300 300 300 /* AU,CG,A,N */ + 300 300 300 300 300 /* AU,CG,A,A */ + 300 300 300 300 300 /* AU,CG,A,C */ + 190 190 190 190 190 /* AU,CG,A,G */ + 300 300 300 300 300 /* AU,CG,A,U */ + 300 300 300 300 300 /* AU,CG,C,N */ + 300 300 300 300 300 /* AU,CG,C,A */ + 300 300 300 300 300 /* AU,CG,C,C */ + 300 300 300 300 300 /* AU,CG,C,G */ + 300 300 300 300 300 /* AU,CG,C,U */ + 300 190 300 190 300 /* AU,CG,G,N */ + 190 190 190 190 190 /* AU,CG,G,A */ + 300 190 300 190 300 /* AU,CG,G,C */ + 190 190 190 190 190 /* AU,CG,G,G */ + 300 190 300 190 300 /* AU,CG,G,U */ + 300 300 300 300 220 /* AU,CG,U,N */ + 300 300 300 300 220 /* AU,CG,U,A */ + 300 300 300 300 220 /* AU,CG,U,C */ + 300 300 300 300 220 /* AU,CG,U,G */ + 220 220 220 220 220 /* AU,CG,U,U */ + 300 300 300 300 300 /* AU,GC,N,N */ + 300 300 300 300 300 /* AU,GC,N,A */ + 300 300 300 300 300 /* AU,GC,N,C */ + 300 300 300 300 300 /* AU,GC,N,G */ + 300 300 300 300 300 /* AU,GC,N,U */ + 300 300 300 300 300 /* AU,GC,A,N */ + 300 300 300 300 300 /* AU,GC,A,A */ + 300 300 300 300 300 /* AU,GC,A,C */ + 190 190 190 190 190 /* AU,GC,A,G */ + 300 300 300 300 300 /* AU,GC,A,U */ + 300 300 300 300 300 /* AU,GC,C,N */ + 300 300 300 300 300 /* AU,GC,C,A */ + 300 300 300 300 300 /* AU,GC,C,C */ + 300 300 300 300 300 /* AU,GC,C,G */ + 300 300 300 300 300 /* AU,GC,C,U */ + 300 190 300 190 300 /* AU,GC,G,N */ + 300 190 300 190 300 /* AU,GC,G,A */ + 300 190 300 190 300 /* AU,GC,G,C */ + 190 190 190 190 190 /* AU,GC,G,G */ + 300 190 300 190 300 /* AU,GC,G,U */ + 300 300 300 300 220 /* AU,GC,U,N */ + 300 300 300 300 220 /* AU,GC,U,A */ + 300 300 300 300 220 /* AU,GC,U,C */ + 300 300 300 300 220 /* AU,GC,U,G */ + 220 220 220 220 220 /* AU,GC,U,U */ + 370 370 370 370 370 /* AU,GU,N,N */ + 370 370 370 370 370 /* AU,GU,N,A */ + 370 370 370 370 370 /* AU,GU,N,C */ + 370 370 370 370 370 /* AU,GU,N,G */ + 370 370 370 370 370 /* AU,GU,N,U */ + 370 370 370 370 370 /* AU,GU,A,N */ + 370 370 370 370 370 /* AU,GU,A,A */ + 370 370 370 370 370 /* AU,GU,A,C */ + 260 260 260 260 260 /* AU,GU,A,G */ + 370 370 370 370 370 /* AU,GU,A,U */ + 370 370 370 370 370 /* AU,GU,C,N */ + 370 370 370 370 370 /* AU,GU,C,A */ + 370 370 370 370 370 /* AU,GU,C,C */ + 370 370 370 370 370 /* AU,GU,C,G */ + 370 370 370 370 370 /* AU,GU,C,U */ + 370 260 370 260 370 /* AU,GU,G,N */ + 370 260 370 260 370 /* AU,GU,G,A */ + 370 260 370 260 370 /* AU,GU,G,C */ + 260 260 260 260 260 /* AU,GU,G,G */ + 370 260 370 260 370 /* AU,GU,G,U */ + 370 370 370 370 300 /* AU,GU,U,N */ + 370 370 370 370 300 /* AU,GU,U,A */ + 370 370 370 370 300 /* AU,GU,U,C */ + 370 370 370 370 300 /* AU,GU,U,G */ + 300 300 300 300 300 /* AU,GU,U,U */ + 370 370 370 370 370 /* AU,UG,N,N */ + 370 370 370 370 370 /* AU,UG,N,A */ + 370 370 370 370 370 /* AU,UG,N,C */ + 370 370 370 370 370 /* AU,UG,N,G */ + 370 370 370 370 370 /* AU,UG,N,U */ + 370 370 370 370 370 /* AU,UG,A,N */ + 370 370 370 370 370 /* AU,UG,A,A */ + 370 370 370 370 370 /* AU,UG,A,C */ + 260 260 260 260 260 /* AU,UG,A,G */ + 370 370 370 370 370 /* AU,UG,A,U */ + 370 370 370 370 370 /* AU,UG,C,N */ + 370 370 370 370 370 /* AU,UG,C,A */ + 370 370 370 370 370 /* AU,UG,C,C */ + 370 370 370 370 370 /* AU,UG,C,G */ + 370 370 370 370 370 /* AU,UG,C,U */ + 370 260 370 260 370 /* AU,UG,G,N */ + 260 260 260 260 260 /* AU,UG,G,A */ + 370 260 370 260 370 /* AU,UG,G,C */ + 260 260 260 260 260 /* AU,UG,G,G */ + 370 260 370 260 370 /* AU,UG,G,U */ + 370 370 370 370 300 /* AU,UG,U,N */ + 370 370 370 370 300 /* AU,UG,U,A */ + 370 370 370 370 300 /* AU,UG,U,C */ + 370 370 370 370 300 /* AU,UG,U,G */ + 300 300 300 300 300 /* AU,UG,U,U */ + 370 370 370 370 370 /* AU,AU,N,N */ + 370 370 370 370 370 /* AU,AU,N,A */ + 370 370 370 370 370 /* AU,AU,N,C */ + 370 370 370 370 370 /* AU,AU,N,G */ + 370 370 370 370 370 /* AU,AU,N,U */ + 370 370 370 370 370 /* AU,AU,A,N */ + 370 370 370 370 370 /* AU,AU,A,A */ + 370 370 370 370 370 /* AU,AU,A,C */ + 260 260 260 260 260 /* AU,AU,A,G */ + 370 370 370 370 370 /* AU,AU,A,U */ + 370 370 370 370 370 /* AU,AU,C,N */ + 370 370 370 370 370 /* AU,AU,C,A */ + 370 370 370 370 370 /* AU,AU,C,C */ + 370 370 370 370 370 /* AU,AU,C,G */ + 370 370 370 370 370 /* AU,AU,C,U */ + 370 260 370 260 370 /* AU,AU,G,N */ + 370 260 370 260 370 /* AU,AU,G,A */ + 370 260 370 260 370 /* AU,AU,G,C */ + 260 260 260 260 260 /* AU,AU,G,G */ + 370 260 370 260 370 /* AU,AU,G,U */ + 370 370 370 370 300 /* AU,AU,U,N */ + 370 370 370 370 300 /* AU,AU,U,A */ + 370 370 370 370 300 /* AU,AU,U,C */ + 370 370 370 370 300 /* AU,AU,U,G */ + 300 300 300 300 300 /* AU,AU,U,U */ + 370 370 370 370 370 /* AU,UA,N,N */ + 370 370 370 370 370 /* AU,UA,N,A */ + 370 370 370 370 370 /* AU,UA,N,C */ + 370 370 370 370 370 /* AU,UA,N,G */ + 370 370 370 370 370 /* AU,UA,N,U */ + 370 370 370 370 370 /* AU,UA,A,N */ + 370 370 370 370 370 /* AU,UA,A,A */ + 370 370 370 370 370 /* AU,UA,A,C */ + 260 260 260 260 260 /* AU,UA,A,G */ + 370 370 370 370 370 /* AU,UA,A,U */ + 370 370 370 370 370 /* AU,UA,C,N */ + 370 370 370 370 370 /* AU,UA,C,A */ + 370 370 370 370 370 /* AU,UA,C,C */ + 370 370 370 370 370 /* AU,UA,C,G */ + 370 370 370 370 370 /* AU,UA,C,U */ + 370 260 370 260 370 /* AU,UA,G,N */ + 260 260 260 260 260 /* AU,UA,G,A */ + 370 260 370 260 370 /* AU,UA,G,C */ + 260 260 260 260 260 /* AU,UA,G,G */ + 370 260 370 260 370 /* AU,UA,G,U */ + 370 370 370 370 300 /* AU,UA,U,N */ + 370 370 370 370 300 /* AU,UA,U,A */ + 370 370 370 370 300 /* AU,UA,U,C */ + 370 370 370 370 300 /* AU,UA,U,G */ + 300 300 300 300 300 /* AU,UA,U,U */ + 370 370 370 370 370 /* AU,NN,N,N */ + 370 370 370 370 370 /* AU,NN,N,A */ + 370 370 370 370 370 /* AU,NN,N,C */ + 370 370 370 370 370 /* AU,NN,N,G */ + 370 370 370 370 370 /* AU,NN,N,U */ + 370 370 370 370 370 /* AU,NN,A,N */ + 370 370 370 370 370 /* AU,NN,A,A */ + 370 370 370 370 370 /* AU,NN,A,C */ + 260 260 260 260 260 /* AU,NN,A,G */ + 370 370 370 370 370 /* AU,NN,A,U */ + 370 370 370 370 370 /* AU,NN,C,N */ + 370 370 370 370 370 /* AU,NN,C,A */ + 370 370 370 370 370 /* AU,NN,C,C */ + 370 370 370 370 370 /* AU,NN,C,G */ + 370 370 370 370 370 /* AU,NN,C,U */ + 370 260 370 260 370 /* AU,NN,G,N */ + 370 260 370 260 370 /* AU,NN,G,A */ + 370 260 370 260 370 /* AU,NN,G,C */ + 260 260 260 260 260 /* AU,NN,G,G */ + 370 260 370 260 370 /* AU,NN,G,U */ + 370 370 370 370 300 /* AU,NN,U,N */ + 370 370 370 370 300 /* AU,NN,U,A */ + 370 370 370 370 300 /* AU,NN,U,C */ + 370 370 370 370 300 /* AU,NN,U,G */ + 300 300 300 300 300 /* AU,NN,U,U */ + 300 300 300 300 300 /* UA,CG,N,N */ + 300 300 300 300 300 /* UA,CG,N,A */ + 300 300 300 300 300 /* UA,CG,N,C */ + 300 300 300 300 300 /* UA,CG,N,G */ + 300 300 300 300 300 /* UA,CG,N,U */ + 300 300 300 190 300 /* UA,CG,A,N */ + 300 300 300 190 300 /* UA,CG,A,A */ + 300 300 300 190 300 /* UA,CG,A,C */ + 190 190 190 190 190 /* UA,CG,A,G */ + 300 300 300 190 300 /* UA,CG,A,U */ + 300 300 300 300 300 /* UA,CG,C,N */ + 300 300 300 300 300 /* UA,CG,C,A */ + 300 300 300 300 300 /* UA,CG,C,C */ + 300 300 300 300 300 /* UA,CG,C,G */ + 300 300 300 300 300 /* UA,CG,C,U */ + 300 190 300 190 300 /* UA,CG,G,N */ + 190 190 190 190 190 /* UA,CG,G,A */ + 300 190 300 190 300 /* UA,CG,G,C */ + 190 190 190 190 190 /* UA,CG,G,G */ + 300 190 300 190 300 /* UA,CG,G,U */ + 300 300 300 300 220 /* UA,CG,U,N */ + 300 300 300 300 220 /* UA,CG,U,A */ + 300 300 300 300 220 /* UA,CG,U,C */ + 300 300 300 300 220 /* UA,CG,U,G */ + 220 220 220 220 220 /* UA,CG,U,U */ + 300 300 300 300 300 /* UA,GC,N,N */ + 300 300 300 300 300 /* UA,GC,N,A */ + 300 300 300 300 300 /* UA,GC,N,C */ + 300 300 300 300 300 /* UA,GC,N,G */ + 300 300 300 300 300 /* UA,GC,N,U */ + 300 300 300 190 300 /* UA,GC,A,N */ + 300 300 300 190 300 /* UA,GC,A,A */ + 300 300 300 190 300 /* UA,GC,A,C */ + 190 190 190 190 190 /* UA,GC,A,G */ + 300 300 300 190 300 /* UA,GC,A,U */ + 300 300 300 300 300 /* UA,GC,C,N */ + 300 300 300 300 300 /* UA,GC,C,A */ + 300 300 300 300 300 /* UA,GC,C,C */ + 300 300 300 300 300 /* UA,GC,C,G */ + 300 300 300 300 300 /* UA,GC,C,U */ + 300 190 300 190 300 /* UA,GC,G,N */ + 300 190 300 190 300 /* UA,GC,G,A */ + 300 190 300 190 300 /* UA,GC,G,C */ + 190 190 190 190 190 /* UA,GC,G,G */ + 300 190 300 190 300 /* UA,GC,G,U */ + 300 300 300 300 220 /* UA,GC,U,N */ + 300 300 300 300 220 /* UA,GC,U,A */ + 300 300 300 300 220 /* UA,GC,U,C */ + 300 300 300 300 220 /* UA,GC,U,G */ + 220 220 220 220 220 /* UA,GC,U,U */ + 370 370 370 370 370 /* UA,GU,N,N */ + 370 370 370 370 370 /* UA,GU,N,A */ + 370 370 370 370 370 /* UA,GU,N,C */ + 370 370 370 370 370 /* UA,GU,N,G */ + 370 370 370 370 370 /* UA,GU,N,U */ + 370 370 370 260 370 /* UA,GU,A,N */ + 370 370 370 260 370 /* UA,GU,A,A */ + 370 370 370 260 370 /* UA,GU,A,C */ + 260 260 260 260 260 /* UA,GU,A,G */ + 370 370 370 260 370 /* UA,GU,A,U */ + 370 370 370 370 370 /* UA,GU,C,N */ + 370 370 370 370 370 /* UA,GU,C,A */ + 370 370 370 370 370 /* UA,GU,C,C */ + 370 370 370 370 370 /* UA,GU,C,G */ + 370 370 370 370 370 /* UA,GU,C,U */ + 370 260 370 260 370 /* UA,GU,G,N */ + 370 260 370 260 370 /* UA,GU,G,A */ + 370 260 370 260 370 /* UA,GU,G,C */ + 260 260 260 260 260 /* UA,GU,G,G */ + 370 260 370 260 370 /* UA,GU,G,U */ + 370 370 370 370 300 /* UA,GU,U,N */ + 370 370 370 370 300 /* UA,GU,U,A */ + 370 370 370 370 300 /* UA,GU,U,C */ + 370 370 370 370 300 /* UA,GU,U,G */ + 300 300 300 300 300 /* UA,GU,U,U */ + 370 370 370 370 370 /* UA,UG,N,N */ + 370 370 370 370 370 /* UA,UG,N,A */ + 370 370 370 370 370 /* UA,UG,N,C */ + 370 370 370 370 370 /* UA,UG,N,G */ + 370 370 370 370 370 /* UA,UG,N,U */ + 370 370 370 260 370 /* UA,UG,A,N */ + 370 370 370 260 370 /* UA,UG,A,A */ + 370 370 370 260 370 /* UA,UG,A,C */ + 260 260 260 260 260 /* UA,UG,A,G */ + 370 370 370 260 370 /* UA,UG,A,U */ + 370 370 370 370 370 /* UA,UG,C,N */ + 370 370 370 370 370 /* UA,UG,C,A */ + 370 370 370 370 370 /* UA,UG,C,C */ + 370 370 370 370 370 /* UA,UG,C,G */ + 370 370 370 370 370 /* UA,UG,C,U */ + 370 260 370 260 370 /* UA,UG,G,N */ + 260 260 260 260 260 /* UA,UG,G,A */ + 370 260 370 260 370 /* UA,UG,G,C */ + 260 260 260 260 260 /* UA,UG,G,G */ + 370 260 370 260 370 /* UA,UG,G,U */ + 370 370 370 370 300 /* UA,UG,U,N */ + 370 370 370 370 300 /* UA,UG,U,A */ + 370 370 370 370 300 /* UA,UG,U,C */ + 370 370 370 370 300 /* UA,UG,U,G */ + 300 300 300 300 300 /* UA,UG,U,U */ + 370 370 370 370 370 /* UA,AU,N,N */ + 370 370 370 370 370 /* UA,AU,N,A */ + 370 370 370 370 370 /* UA,AU,N,C */ + 370 370 370 370 370 /* UA,AU,N,G */ + 370 370 370 370 370 /* UA,AU,N,U */ + 370 370 370 260 370 /* UA,AU,A,N */ + 370 370 370 260 370 /* UA,AU,A,A */ + 370 370 370 260 370 /* UA,AU,A,C */ + 260 260 260 260 260 /* UA,AU,A,G */ + 370 370 370 260 370 /* UA,AU,A,U */ + 370 370 370 370 370 /* UA,AU,C,N */ + 370 370 370 370 370 /* UA,AU,C,A */ + 370 370 370 370 370 /* UA,AU,C,C */ + 370 370 370 370 370 /* UA,AU,C,G */ + 370 370 370 370 370 /* UA,AU,C,U */ + 370 260 370 260 370 /* UA,AU,G,N */ + 370 260 370 260 370 /* UA,AU,G,A */ + 370 260 370 260 370 /* UA,AU,G,C */ + 260 260 260 260 260 /* UA,AU,G,G */ + 370 260 370 260 370 /* UA,AU,G,U */ + 370 370 370 370 300 /* UA,AU,U,N */ + 370 370 370 370 300 /* UA,AU,U,A */ + 370 370 370 370 300 /* UA,AU,U,C */ + 370 370 370 370 300 /* UA,AU,U,G */ + 300 300 300 300 300 /* UA,AU,U,U */ + 370 370 370 370 370 /* UA,UA,N,N */ + 370 370 370 370 370 /* UA,UA,N,A */ + 370 370 370 370 370 /* UA,UA,N,C */ + 370 370 370 370 370 /* UA,UA,N,G */ + 370 370 370 370 370 /* UA,UA,N,U */ + 370 370 370 260 370 /* UA,UA,A,N */ + 370 370 370 260 370 /* UA,UA,A,A */ + 370 370 370 260 370 /* UA,UA,A,C */ + 260 260 260 260 260 /* UA,UA,A,G */ + 370 370 370 260 370 /* UA,UA,A,U */ + 370 370 370 370 370 /* UA,UA,C,N */ + 370 370 370 370 370 /* UA,UA,C,A */ + 370 370 370 370 370 /* UA,UA,C,C */ + 370 370 370 370 370 /* UA,UA,C,G */ + 370 370 370 370 370 /* UA,UA,C,U */ + 370 260 370 260 370 /* UA,UA,G,N */ + 260 260 260 260 260 /* UA,UA,G,A */ + 370 260 370 260 370 /* UA,UA,G,C */ + 260 260 260 260 260 /* UA,UA,G,G */ + 370 260 370 260 370 /* UA,UA,G,U */ + 370 370 370 370 300 /* UA,UA,U,N */ + 370 370 370 370 300 /* UA,UA,U,A */ + 370 370 370 370 300 /* UA,UA,U,C */ + 370 370 370 370 300 /* UA,UA,U,G */ + 300 300 300 300 300 /* UA,UA,U,U */ + 370 370 370 370 370 /* UA,NN,N,N */ + 370 370 370 370 370 /* UA,NN,N,A */ + 370 370 370 370 370 /* UA,NN,N,C */ + 370 370 370 370 370 /* UA,NN,N,G */ + 370 370 370 370 370 /* UA,NN,N,U */ + 370 370 370 260 370 /* UA,NN,A,N */ + 370 370 370 260 370 /* UA,NN,A,A */ + 370 370 370 260 370 /* UA,NN,A,C */ + 260 260 260 260 260 /* UA,NN,A,G */ + 370 370 370 260 370 /* UA,NN,A,U */ + 370 370 370 370 370 /* UA,NN,C,N */ + 370 370 370 370 370 /* UA,NN,C,A */ + 370 370 370 370 370 /* UA,NN,C,C */ + 370 370 370 370 370 /* UA,NN,C,G */ + 370 370 370 370 370 /* UA,NN,C,U */ + 370 260 370 260 370 /* UA,NN,G,N */ + 370 260 370 260 370 /* UA,NN,G,A */ + 370 260 370 260 370 /* UA,NN,G,C */ + 260 260 260 260 260 /* UA,NN,G,G */ + 370 260 370 260 370 /* UA,NN,G,U */ + 370 370 370 370 300 /* UA,NN,U,N */ + 370 370 370 370 300 /* UA,NN,U,A */ + 370 370 370 370 300 /* UA,NN,U,C */ + 370 370 370 370 300 /* UA,NN,U,G */ + 300 300 300 300 300 /* UA,NN,U,U */ + 300 300 300 300 300 /* NN,CG,N,N */ + 300 300 300 300 300 /* NN,CG,N,A */ + 300 300 300 300 300 /* NN,CG,N,C */ + 300 300 300 300 300 /* NN,CG,N,G */ + 300 300 300 300 300 /* NN,CG,N,U */ + 300 300 300 300 300 /* NN,CG,A,N */ + 300 300 300 300 300 /* NN,CG,A,A */ + 300 300 300 300 300 /* NN,CG,A,C */ + 190 190 190 190 190 /* NN,CG,A,G */ + 300 300 300 300 300 /* NN,CG,A,U */ + 300 300 300 300 300 /* NN,CG,C,N */ + 300 300 300 300 300 /* NN,CG,C,A */ + 300 300 300 300 300 /* NN,CG,C,C */ + 300 300 300 300 300 /* NN,CG,C,G */ + 300 300 300 300 300 /* NN,CG,C,U */ + 300 190 300 190 300 /* NN,CG,G,N */ + 190 190 190 190 190 /* NN,CG,G,A */ + 300 190 300 190 300 /* NN,CG,G,C */ + 190 190 190 190 190 /* NN,CG,G,G */ + 300 190 300 190 300 /* NN,CG,G,U */ + 300 300 300 300 220 /* NN,CG,U,N */ + 300 300 300 300 220 /* NN,CG,U,A */ + 300 300 300 300 220 /* NN,CG,U,C */ + 300 300 300 300 220 /* NN,CG,U,G */ + 220 220 220 220 220 /* NN,CG,U,U */ + 300 300 300 300 300 /* NN,GC,N,N */ + 300 300 300 300 300 /* NN,GC,N,A */ + 300 300 300 300 300 /* NN,GC,N,C */ + 300 300 300 300 300 /* NN,GC,N,G */ + 300 300 300 300 300 /* NN,GC,N,U */ + 300 300 300 300 300 /* NN,GC,A,N */ + 300 300 300 300 300 /* NN,GC,A,A */ + 300 300 300 300 300 /* NN,GC,A,C */ + 190 190 190 190 190 /* NN,GC,A,G */ + 300 300 300 300 300 /* NN,GC,A,U */ + 300 300 300 300 300 /* NN,GC,C,N */ + 300 300 300 300 300 /* NN,GC,C,A */ + 300 300 300 300 300 /* NN,GC,C,C */ + 300 300 300 300 300 /* NN,GC,C,G */ + 300 300 300 300 300 /* NN,GC,C,U */ + 300 190 300 190 300 /* NN,GC,G,N */ + 300 190 300 190 300 /* NN,GC,G,A */ + 300 190 300 190 300 /* NN,GC,G,C */ + 190 190 190 190 190 /* NN,GC,G,G */ + 300 190 300 190 300 /* NN,GC,G,U */ + 300 300 300 300 220 /* NN,GC,U,N */ + 300 300 300 300 220 /* NN,GC,U,A */ + 300 300 300 300 220 /* NN,GC,U,C */ + 300 300 300 300 220 /* NN,GC,U,G */ + 220 220 220 220 220 /* NN,GC,U,U */ + 370 370 370 370 370 /* NN,GU,N,N */ + 370 370 370 370 370 /* NN,GU,N,A */ + 370 370 370 370 370 /* NN,GU,N,C */ + 370 370 370 370 370 /* NN,GU,N,G */ + 370 370 370 370 370 /* NN,GU,N,U */ + 370 370 370 370 370 /* NN,GU,A,N */ + 370 370 370 370 370 /* NN,GU,A,A */ + 370 370 370 370 370 /* NN,GU,A,C */ + 260 260 260 260 260 /* NN,GU,A,G */ + 370 370 370 370 370 /* NN,GU,A,U */ + 370 370 370 370 370 /* NN,GU,C,N */ + 370 370 370 370 370 /* NN,GU,C,A */ + 370 370 370 370 370 /* NN,GU,C,C */ + 370 370 370 370 370 /* NN,GU,C,G */ + 370 370 370 370 370 /* NN,GU,C,U */ + 370 260 370 260 370 /* NN,GU,G,N */ + 370 260 370 260 370 /* NN,GU,G,A */ + 370 260 370 260 370 /* NN,GU,G,C */ + 260 260 260 260 260 /* NN,GU,G,G */ + 370 260 370 260 370 /* NN,GU,G,U */ + 370 370 370 370 300 /* NN,GU,U,N */ + 370 370 370 370 300 /* NN,GU,U,A */ + 370 370 370 370 300 /* NN,GU,U,C */ + 370 370 370 370 300 /* NN,GU,U,G */ + 300 300 300 300 300 /* NN,GU,U,U */ + 370 370 370 370 370 /* NN,UG,N,N */ + 370 370 370 370 370 /* NN,UG,N,A */ + 370 370 370 370 370 /* NN,UG,N,C */ + 370 370 370 370 370 /* NN,UG,N,G */ + 370 370 370 370 370 /* NN,UG,N,U */ + 370 370 370 370 370 /* NN,UG,A,N */ + 370 370 370 370 370 /* NN,UG,A,A */ + 370 370 370 370 370 /* NN,UG,A,C */ + 260 260 260 260 260 /* NN,UG,A,G */ + 370 370 370 370 370 /* NN,UG,A,U */ + 370 370 370 370 370 /* NN,UG,C,N */ + 370 370 370 370 370 /* NN,UG,C,A */ + 370 370 370 370 370 /* NN,UG,C,C */ + 370 370 370 370 370 /* NN,UG,C,G */ + 370 370 370 370 370 /* NN,UG,C,U */ + 370 260 370 260 370 /* NN,UG,G,N */ + 260 260 260 260 260 /* NN,UG,G,A */ + 370 260 370 260 370 /* NN,UG,G,C */ + 260 260 260 260 260 /* NN,UG,G,G */ + 370 260 370 260 370 /* NN,UG,G,U */ + 370 370 370 370 300 /* NN,UG,U,N */ + 370 370 370 370 300 /* NN,UG,U,A */ + 370 370 370 370 300 /* NN,UG,U,C */ + 370 370 370 370 300 /* NN,UG,U,G */ + 300 300 300 300 300 /* NN,UG,U,U */ + 370 370 370 370 370 /* NN,AU,N,N */ + 370 370 370 370 370 /* NN,AU,N,A */ + 370 370 370 370 370 /* NN,AU,N,C */ + 370 370 370 370 370 /* NN,AU,N,G */ + 370 370 370 370 370 /* NN,AU,N,U */ + 370 370 370 370 370 /* NN,AU,A,N */ + 370 370 370 370 370 /* NN,AU,A,A */ + 370 370 370 370 370 /* NN,AU,A,C */ + 260 260 260 260 260 /* NN,AU,A,G */ + 370 370 370 370 370 /* NN,AU,A,U */ + 370 370 370 370 370 /* NN,AU,C,N */ + 370 370 370 370 370 /* NN,AU,C,A */ + 370 370 370 370 370 /* NN,AU,C,C */ + 370 370 370 370 370 /* NN,AU,C,G */ + 370 370 370 370 370 /* NN,AU,C,U */ + 370 260 370 260 370 /* NN,AU,G,N */ + 370 260 370 260 370 /* NN,AU,G,A */ + 370 260 370 260 370 /* NN,AU,G,C */ + 260 260 260 260 260 /* NN,AU,G,G */ + 370 260 370 260 370 /* NN,AU,G,U */ + 370 370 370 370 300 /* NN,AU,U,N */ + 370 370 370 370 300 /* NN,AU,U,A */ + 370 370 370 370 300 /* NN,AU,U,C */ + 370 370 370 370 300 /* NN,AU,U,G */ + 300 300 300 300 300 /* NN,AU,U,U */ + 370 370 370 370 370 /* NN,UA,N,N */ + 370 370 370 370 370 /* NN,UA,N,A */ + 370 370 370 370 370 /* NN,UA,N,C */ + 370 370 370 370 370 /* NN,UA,N,G */ + 370 370 370 370 370 /* NN,UA,N,U */ + 370 370 370 370 370 /* NN,UA,A,N */ + 370 370 370 370 370 /* NN,UA,A,A */ + 370 370 370 370 370 /* NN,UA,A,C */ + 260 260 260 260 260 /* NN,UA,A,G */ + 370 370 370 370 370 /* NN,UA,A,U */ + 370 370 370 370 370 /* NN,UA,C,N */ + 370 370 370 370 370 /* NN,UA,C,A */ + 370 370 370 370 370 /* NN,UA,C,C */ + 370 370 370 370 370 /* NN,UA,C,G */ + 370 370 370 370 370 /* NN,UA,C,U */ + 370 260 370 260 370 /* NN,UA,G,N */ + 260 260 260 260 260 /* NN,UA,G,A */ + 370 260 370 260 370 /* NN,UA,G,C */ + 260 260 260 260 260 /* NN,UA,G,G */ + 370 260 370 260 370 /* NN,UA,G,U */ + 370 370 370 370 300 /* NN,UA,U,N */ + 370 370 370 370 300 /* NN,UA,U,A */ + 370 370 370 370 300 /* NN,UA,U,C */ + 370 370 370 370 300 /* NN,UA,U,G */ + 300 300 300 300 300 /* NN,UA,U,U */ + 370 370 370 370 370 /* NN,NN,N,N */ + 370 370 370 370 370 /* NN,NN,N,A */ + 370 370 370 370 370 /* NN,NN,N,C */ + 370 370 370 370 370 /* NN,NN,N,G */ + 370 370 370 370 370 /* NN,NN,N,U */ + 370 370 370 370 370 /* NN,NN,A,N */ + 370 370 370 370 370 /* NN,NN,A,A */ + 370 370 370 370 370 /* NN,NN,A,C */ + 260 260 260 260 260 /* NN,NN,A,G */ + 370 370 370 370 370 /* NN,NN,A,U */ + 370 370 370 370 370 /* NN,NN,C,N */ + 370 370 370 370 370 /* NN,NN,C,A */ + 370 370 370 370 370 /* NN,NN,C,C */ + 370 370 370 370 370 /* NN,NN,C,G */ + 370 370 370 370 370 /* NN,NN,C,U */ + 370 260 370 260 370 /* NN,NN,G,N */ + 370 260 370 260 370 /* NN,NN,G,A */ + 370 260 370 260 370 /* NN,NN,G,C */ + 260 260 260 260 260 /* NN,NN,G,G */ + 370 260 370 260 370 /* NN,NN,G,U */ + 370 370 370 370 300 /* NN,NN,U,N */ + 370 370 370 370 300 /* NN,NN,U,A */ + 370 370 370 370 300 /* NN,NN,U,C */ + 370 370 370 370 300 /* NN,NN,U,G */ + 300 300 300 300 300 /* NN,NN,U,U */ + +# int21_enthalpies + 350 350 350 350 350 /* CG,CG,N,N */ + 350 350 350 350 350 /* CG,CG,N,A */ + 350 350 350 350 350 /* CG,CG,N,C */ + 350 350 350 350 350 /* CG,CG,N,G */ + 350 350 350 350 350 /* CG,CG,N,U */ + 350 350 350 -230 350 /* CG,CG,A,N */ + 350 350 350 -230 350 /* CG,CG,A,A */ + 350 350 350 -230 350 /* CG,CG,A,C */ + -230 -230 -230 -230 -230 /* CG,CG,A,G */ + 350 350 350 -230 350 /* CG,CG,A,U */ + 350 350 350 350 350 /* CG,CG,C,N */ + 350 350 350 350 350 /* CG,CG,C,A */ + 350 350 350 350 350 /* CG,CG,C,C */ + 350 350 350 350 350 /* CG,CG,C,G */ + 350 350 350 350 350 /* CG,CG,C,U */ + 350 -230 350 -230 350 /* CG,CG,G,N */ + -230 -230 -230 -230 -230 /* CG,CG,G,A */ + 350 -230 350 -230 350 /* CG,CG,G,C */ + -230 -230 -230 -230 -230 /* CG,CG,G,G */ + 350 -230 350 -230 350 /* CG,CG,G,U */ + 350 350 350 350 -670 /* CG,CG,U,N */ + 350 350 350 350 -670 /* CG,CG,U,A */ + 350 350 350 350 -670 /* CG,CG,U,C */ + 350 350 350 350 -670 /* CG,CG,U,G */ + -670 -670 -670 -670 -670 /* CG,CG,U,U */ + 780 640 780 350 350 /* CG,GC,N,N */ + 350 350 350 350 350 /* CG,GC,N,A */ + 780 350 780 350 350 /* CG,GC,N,C */ + 350 350 350 350 350 /* CG,GC,N,G */ + 640 640 350 350 350 /* CG,GC,N,U */ + 350 350 350 250 350 /* CG,GC,A,N */ + 350 260 350 250 350 /* CG,GC,A,A */ + 350 350 -250 -230 350 /* CG,GC,A,C */ + -230 -230 -230 -230 -230 /* CG,GC,A,G */ + 350 350 350 -230 350 /* CG,GC,A,U */ + 780 640 780 350 350 /* CG,GC,C,N */ + 350 160 350 350 350 /* CG,GC,C,A */ + 780 350 780 350 350 /* CG,GC,C,C */ + 350 350 350 350 350 /* CG,GC,C,G */ + 640 640 350 350 350 /* CG,GC,C,U */ + 350 -160 350 -230 350 /* CG,GC,G,N */ + 350 -160 350 -410 350 /* CG,GC,G,A */ + 350 -230 350 -230 350 /* CG,GC,G,C */ + -230 -310 -230 -230 -230 /* CG,GC,G,G */ + 350 -230 350 -230 350 /* CG,GC,G,U */ + 580 350 580 350 -580 /* CG,GC,U,N */ + 350 350 350 350 -670 /* CG,GC,U,A */ + 580 350 580 350 -580 /* CG,GC,U,C */ + 350 350 350 350 -670 /* CG,GC,U,G */ + -670 -670 -690 -670 -700 /* CG,GC,U,U */ + 850 850 850 850 850 /* CG,GU,N,N */ + 850 850 850 850 850 /* CG,GU,N,A */ + 850 850 850 850 850 /* CG,GU,N,C */ + 850 850 850 850 850 /* CG,GU,N,G */ + 850 850 850 850 850 /* CG,GU,N,U */ + 850 850 850 280 850 /* CG,GU,A,N */ + 850 850 850 280 850 /* CG,GU,A,A */ + 850 850 850 280 850 /* CG,GU,A,C */ + 280 280 280 280 280 /* CG,GU,A,G */ + 850 850 850 280 850 /* CG,GU,A,U */ + 850 850 850 850 850 /* CG,GU,C,N */ + 850 850 850 850 850 /* CG,GU,C,A */ + 850 850 850 850 850 /* CG,GU,C,C */ + 850 850 850 850 850 /* CG,GU,C,G */ + 850 850 850 850 850 /* CG,GU,C,U */ + 850 280 850 280 850 /* CG,GU,G,N */ + 850 280 850 280 850 /* CG,GU,G,A */ + 850 280 850 280 850 /* CG,GU,G,C */ + 280 280 280 280 280 /* CG,GU,G,G */ + 850 280 850 280 850 /* CG,GU,G,U */ + 850 850 850 850 -160 /* CG,GU,U,N */ + 850 850 850 850 -160 /* CG,GU,U,A */ + 850 850 850 850 -160 /* CG,GU,U,C */ + 850 850 850 850 -160 /* CG,GU,U,G */ + -160 -160 -160 -160 -160 /* CG,GU,U,U */ + 850 850 850 850 850 /* CG,UG,N,N */ + 850 850 850 850 850 /* CG,UG,N,A */ + 850 850 850 850 850 /* CG,UG,N,C */ + 850 850 850 850 850 /* CG,UG,N,G */ + 850 850 850 850 850 /* CG,UG,N,U */ + 850 850 850 280 850 /* CG,UG,A,N */ + 850 850 850 280 850 /* CG,UG,A,A */ + 850 850 850 280 850 /* CG,UG,A,C */ + 280 280 280 280 280 /* CG,UG,A,G */ + 850 850 850 280 850 /* CG,UG,A,U */ + 850 850 850 850 850 /* CG,UG,C,N */ + 850 850 850 850 850 /* CG,UG,C,A */ + 850 850 850 850 850 /* CG,UG,C,C */ + 850 850 850 850 850 /* CG,UG,C,G */ + 850 850 850 850 850 /* CG,UG,C,U */ + 850 280 850 280 850 /* CG,UG,G,N */ + 280 280 280 280 280 /* CG,UG,G,A */ + 850 280 850 280 850 /* CG,UG,G,C */ + 280 280 280 280 280 /* CG,UG,G,G */ + 850 280 850 280 850 /* CG,UG,G,U */ + 850 850 850 850 -160 /* CG,UG,U,N */ + 850 850 850 850 -160 /* CG,UG,U,A */ + 850 850 850 850 -160 /* CG,UG,U,C */ + 850 850 850 850 -160 /* CG,UG,U,G */ + -160 -160 -160 -160 -160 /* CG,UG,U,U */ + 850 850 850 850 850 /* CG,AU,N,N */ + 850 850 850 850 850 /* CG,AU,N,A */ + 850 850 850 850 850 /* CG,AU,N,C */ + 850 850 850 850 850 /* CG,AU,N,G */ + 850 850 850 850 850 /* CG,AU,N,U */ + 850 850 850 280 850 /* CG,AU,A,N */ + 850 850 850 280 850 /* CG,AU,A,A */ + 850 850 850 280 850 /* CG,AU,A,C */ + 280 280 280 280 280 /* CG,AU,A,G */ + 850 850 850 280 850 /* CG,AU,A,U */ + 850 850 850 850 850 /* CG,AU,C,N */ + 850 850 850 850 850 /* CG,AU,C,A */ + 850 850 850 850 850 /* CG,AU,C,C */ + 850 850 850 850 850 /* CG,AU,C,G */ + 850 850 850 850 850 /* CG,AU,C,U */ + 850 280 850 280 850 /* CG,AU,G,N */ + 850 280 850 280 850 /* CG,AU,G,A */ + 850 280 850 280 850 /* CG,AU,G,C */ + 280 280 280 280 280 /* CG,AU,G,G */ + 850 280 850 280 850 /* CG,AU,G,U */ + 850 850 850 850 -160 /* CG,AU,U,N */ + 850 850 850 850 -160 /* CG,AU,U,A */ + 850 850 850 850 -160 /* CG,AU,U,C */ + 850 850 850 850 -160 /* CG,AU,U,G */ + -160 -160 -160 -160 -160 /* CG,AU,U,U */ + 850 850 850 850 850 /* CG,UA,N,N */ + 850 850 850 850 850 /* CG,UA,N,A */ + 850 850 850 850 850 /* CG,UA,N,C */ + 850 850 850 850 850 /* CG,UA,N,G */ + 850 850 850 850 850 /* CG,UA,N,U */ + 850 850 850 280 850 /* CG,UA,A,N */ + 850 850 850 280 850 /* CG,UA,A,A */ + 850 850 850 280 850 /* CG,UA,A,C */ + 280 280 280 280 280 /* CG,UA,A,G */ + 850 850 850 280 850 /* CG,UA,A,U */ + 850 850 850 850 850 /* CG,UA,C,N */ + 850 850 850 850 850 /* CG,UA,C,A */ + 850 850 850 850 850 /* CG,UA,C,C */ + 850 850 850 850 850 /* CG,UA,C,G */ + 850 850 850 850 850 /* CG,UA,C,U */ + 850 280 850 280 850 /* CG,UA,G,N */ + 280 280 280 280 280 /* CG,UA,G,A */ + 850 280 850 280 850 /* CG,UA,G,C */ + 280 280 280 280 280 /* CG,UA,G,G */ + 850 280 850 280 850 /* CG,UA,G,U */ + 850 850 850 850 -160 /* CG,UA,U,N */ + 850 850 850 850 -160 /* CG,UA,U,A */ + 850 850 850 850 -160 /* CG,UA,U,C */ + 850 850 850 850 -160 /* CG,UA,U,G */ + -160 -160 -160 -160 -160 /* CG,UA,U,U */ + 850 850 850 850 850 /* CG,NN,N,N */ + 850 850 850 850 850 /* CG,NN,N,A */ + 850 850 850 850 850 /* CG,NN,N,C */ + 850 850 850 850 850 /* CG,NN,N,G */ + 850 850 850 850 850 /* CG,NN,N,U */ + 850 850 850 280 850 /* CG,NN,A,N */ + 850 850 850 280 850 /* CG,NN,A,A */ + 850 850 850 280 850 /* CG,NN,A,C */ + 280 280 280 280 280 /* CG,NN,A,G */ + 850 850 850 280 850 /* CG,NN,A,U */ + 850 850 850 850 850 /* CG,NN,C,N */ + 850 850 850 850 850 /* CG,NN,C,A */ + 850 850 850 850 850 /* CG,NN,C,C */ + 850 850 850 850 850 /* CG,NN,C,G */ + 850 850 850 850 850 /* CG,NN,C,U */ + 850 280 850 280 850 /* CG,NN,G,N */ + 850 280 850 280 850 /* CG,NN,G,A */ + 850 280 850 280 850 /* CG,NN,G,C */ + 280 280 280 280 280 /* CG,NN,G,G */ + 850 280 850 280 850 /* CG,NN,G,U */ + 850 850 850 850 -160 /* CG,NN,U,N */ + 850 850 850 850 -160 /* CG,NN,U,A */ + 850 850 850 850 -160 /* CG,NN,U,C */ + 850 850 850 850 -160 /* CG,NN,U,G */ + -160 -160 -160 -160 -160 /* CG,NN,U,U */ + 690 690 350 350 350 /* GC,CG,N,N */ + 690 690 350 350 350 /* GC,CG,N,A */ + 350 350 350 350 350 /* GC,CG,N,C */ + 350 350 350 350 350 /* GC,CG,N,G */ + 350 350 350 350 350 /* GC,CG,N,U */ + 690 690 350 350 350 /* GC,CG,A,N */ + 690 690 350 240 350 /* GC,CG,A,A */ + 350 350 350 350 350 /* GC,CG,A,C */ + -230 -500 -230 -230 -230 /* GC,CG,A,G */ + 350 350 350 350 350 /* GC,CG,A,U */ + 350 350 350 350 350 /* GC,CG,C,N */ + 350 350 350 350 350 /* GC,CG,C,A */ + 350 350 350 350 350 /* GC,CG,C,C */ + 350 350 350 350 350 /* GC,CG,C,G */ + 350 350 130 350 350 /* GC,CG,C,U */ + 350 -230 350 -230 350 /* GC,CG,G,N */ + -230 -230 -230 -230 -230 /* GC,CG,G,A */ + 350 -230 350 -230 350 /* GC,CG,G,C */ + -230 -230 -230 -230 -230 /* GC,CG,G,G */ + 350 -230 350 -230 350 /* GC,CG,G,U */ + 350 350 350 350 -670 /* GC,CG,U,N */ + 350 350 350 350 -670 /* GC,CG,U,A */ + 350 350 350 350 -670 /* GC,CG,U,C */ + 350 350 350 350 -670 /* GC,CG,U,G */ + -670 -670 -670 -670 -670 /* GC,CG,U,U */ + 350 350 350 350 350 /* GC,GC,N,N */ + 350 350 350 350 350 /* GC,GC,N,A */ + 350 350 350 350 350 /* GC,GC,N,C */ + 350 350 350 350 350 /* GC,GC,N,G */ + 350 350 350 350 350 /* GC,GC,N,U */ + 350 350 350 350 350 /* GC,GC,A,N */ + 350 350 350 350 350 /* GC,GC,A,A */ + 350 350 350 350 350 /* GC,GC,A,C */ + -230 -230 -230 -230 -230 /* GC,GC,A,G */ + 350 350 350 350 350 /* GC,GC,A,U */ + 350 350 350 350 350 /* GC,GC,C,N */ + 350 350 350 350 350 /* GC,GC,C,A */ + 350 350 350 350 350 /* GC,GC,C,C */ + 350 350 350 350 350 /* GC,GC,C,G */ + 350 350 350 350 350 /* GC,GC,C,U */ + 350 -230 350 -230 350 /* GC,GC,G,N */ + 350 -230 350 -230 350 /* GC,GC,G,A */ + 350 -230 350 -230 350 /* GC,GC,G,C */ + -230 -230 -230 -230 -230 /* GC,GC,G,G */ + 350 -230 350 -230 350 /* GC,GC,G,U */ + 350 350 350 350 -670 /* GC,GC,U,N */ + 350 350 350 350 -670 /* GC,GC,U,A */ + 350 350 350 350 -670 /* GC,GC,U,C */ + 350 350 350 350 -670 /* GC,GC,U,G */ + -670 -670 -670 -670 -670 /* GC,GC,U,U */ + 850 850 850 850 850 /* GC,GU,N,N */ + 850 850 850 850 850 /* GC,GU,N,A */ + 850 850 850 850 850 /* GC,GU,N,C */ + 850 850 850 850 850 /* GC,GU,N,G */ + 850 850 850 850 850 /* GC,GU,N,U */ + 850 850 850 850 850 /* GC,GU,A,N */ + 850 850 850 850 850 /* GC,GU,A,A */ + 850 850 850 850 850 /* GC,GU,A,C */ + 280 280 280 280 280 /* GC,GU,A,G */ + 850 850 850 850 850 /* GC,GU,A,U */ + 850 850 850 850 850 /* GC,GU,C,N */ + 850 850 850 850 850 /* GC,GU,C,A */ + 850 850 850 850 850 /* GC,GU,C,C */ + 850 850 850 850 850 /* GC,GU,C,G */ + 850 850 850 850 850 /* GC,GU,C,U */ + 850 280 850 280 850 /* GC,GU,G,N */ + 850 280 850 280 850 /* GC,GU,G,A */ + 850 280 850 280 850 /* GC,GU,G,C */ + 280 280 280 280 280 /* GC,GU,G,G */ + 850 280 850 280 850 /* GC,GU,G,U */ + 850 850 850 850 -160 /* GC,GU,U,N */ + 850 850 850 850 -160 /* GC,GU,U,A */ + 850 850 850 850 -160 /* GC,GU,U,C */ + 850 850 850 850 -160 /* GC,GU,U,G */ + -160 -160 -160 -160 -160 /* GC,GU,U,U */ + 850 850 850 850 850 /* GC,UG,N,N */ + 850 850 850 850 850 /* GC,UG,N,A */ + 850 850 850 850 850 /* GC,UG,N,C */ + 850 850 850 850 850 /* GC,UG,N,G */ + 850 850 850 850 850 /* GC,UG,N,U */ + 850 850 850 850 850 /* GC,UG,A,N */ + 850 690 850 240 850 /* GC,UG,A,A */ + 850 850 850 850 850 /* GC,UG,A,C */ + 280 -500 280 280 280 /* GC,UG,A,G */ + 850 850 850 850 850 /* GC,UG,A,U */ + 850 850 850 850 850 /* GC,UG,C,N */ + 850 850 850 850 850 /* GC,UG,C,A */ + 850 850 850 850 850 /* GC,UG,C,C */ + 850 850 850 850 850 /* GC,UG,C,G */ + 850 850 130 850 850 /* GC,UG,C,U */ + 850 280 850 280 850 /* GC,UG,G,N */ + 280 280 280 280 280 /* GC,UG,G,A */ + 850 280 850 280 850 /* GC,UG,G,C */ + 280 280 280 280 280 /* GC,UG,G,G */ + 850 280 850 280 850 /* 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UA,GC,C,C */ + 850 850 850 850 850 /* UA,GC,C,G */ + 850 850 850 850 850 /* UA,GC,C,U */ + 850 280 850 280 850 /* UA,GC,G,N */ + 850 280 850 280 850 /* UA,GC,G,A */ + 850 280 850 280 850 /* UA,GC,G,C */ + 280 280 280 280 280 /* UA,GC,G,G */ + 850 280 850 280 850 /* UA,GC,G,U */ + 850 850 850 850 -160 /* UA,GC,U,N */ + 850 850 850 850 -160 /* UA,GC,U,A */ + 850 850 850 850 -160 /* UA,GC,U,C */ + 850 850 850 850 -160 /* UA,GC,U,G */ + -160 -160 -160 -160 -160 /* UA,GC,U,U */ + 1350 1350 1350 1350 1350 /* UA,GU,N,N */ + 1350 1350 1350 1350 1350 /* UA,GU,N,A */ + 1350 1350 1350 1350 1350 /* UA,GU,N,C */ + 1350 1350 1350 1350 1350 /* UA,GU,N,G */ + 1350 1350 1350 1350 1350 /* UA,GU,N,U */ + 1350 1350 1350 780 1350 /* UA,GU,A,N */ + 1350 1350 1350 780 1350 /* UA,GU,A,A */ + 1350 1350 1350 780 1350 /* UA,GU,A,C */ + 780 780 780 780 780 /* UA,GU,A,G */ + 1350 1350 1350 780 1350 /* UA,GU,A,U */ + 1350 1350 1350 1350 1350 /* UA,GU,C,N */ + 1350 1350 1350 1350 1350 /* UA,GU,C,A */ + 1350 1350 1350 1350 1350 /* UA,GU,C,C */ + 1350 1350 1350 1350 1350 /* UA,GU,C,G */ + 1350 1350 1350 1350 1350 /* UA,GU,C,U */ + 1350 780 1350 780 1350 /* UA,GU,G,N */ + 1350 780 1350 780 1350 /* UA,GU,G,A */ + 1350 780 1350 780 1350 /* UA,GU,G,C */ + 780 780 780 780 780 /* UA,GU,G,G */ + 1350 780 1350 780 1350 /* UA,GU,G,U */ + 1350 1350 1350 1350 340 /* UA,GU,U,N */ + 1350 1350 1350 1350 340 /* UA,GU,U,A */ + 1350 1350 1350 1350 340 /* UA,GU,U,C */ + 1350 1350 1350 1350 340 /* UA,GU,U,G */ + 340 340 340 340 340 /* UA,GU,U,U */ + 1350 1350 1350 1350 1350 /* UA,UG,N,N */ + 1350 1350 1350 1350 1350 /* UA,UG,N,A */ + 1350 1350 1350 1350 1350 /* UA,UG,N,C */ + 1350 1350 1350 1350 1350 /* UA,UG,N,G */ + 1350 1350 1350 1350 1350 /* UA,UG,N,U */ + 1350 1350 1350 780 1350 /* UA,UG,A,N */ + 1350 1350 1350 780 1350 /* UA,UG,A,A */ + 1350 1350 1350 780 1350 /* UA,UG,A,C */ + 780 780 780 780 780 /* UA,UG,A,G */ + 1350 1350 1350 780 1350 /* UA,UG,A,U */ + 1350 1350 1350 1350 1350 /* UA,UG,C,N */ + 1350 1350 1350 1350 1350 /* UA,UG,C,A */ + 1350 1350 1350 1350 1350 /* UA,UG,C,C */ + 1350 1350 1350 1350 1350 /* UA,UG,C,G */ + 1350 1350 1350 1350 1350 /* UA,UG,C,U */ + 1350 780 1350 780 1350 /* UA,UG,G,N */ + 780 780 780 780 780 /* UA,UG,G,A */ + 1350 780 1350 780 1350 /* UA,UG,G,C */ + 780 780 780 780 780 /* UA,UG,G,G */ + 1350 780 1350 780 1350 /* UA,UG,G,U */ + 1350 1350 1350 1350 340 /* UA,UG,U,N */ + 1350 1350 1350 1350 340 /* UA,UG,U,A */ + 1350 1350 1350 1350 340 /* UA,UG,U,C */ + 1350 1350 1350 1350 340 /* UA,UG,U,G */ + 340 340 340 340 340 /* UA,UG,U,U */ + 1350 1350 1350 1350 1350 /* UA,AU,N,N */ + 1350 1350 1350 1350 1350 /* UA,AU,N,A */ + 1350 1350 1350 1350 1350 /* UA,AU,N,C */ + 1350 1350 1350 1350 1350 /* UA,AU,N,G */ + 1350 1350 1350 1350 1350 /* UA,AU,N,U */ + 1350 1350 1350 780 1350 /* UA,AU,A,N */ + 1350 1350 1350 780 1350 /* UA,AU,A,A */ + 1350 1350 1350 780 1350 /* UA,AU,A,C */ + 780 780 780 780 780 /* UA,AU,A,G */ + 1350 1350 1350 780 1350 /* UA,AU,A,U */ + 1350 1350 1350 1350 1350 /* UA,AU,C,N */ + 1350 1350 1350 1350 1350 /* UA,AU,C,A */ + 1350 1350 1350 1350 1350 /* UA,AU,C,C */ + 1350 1350 1350 1350 1350 /* UA,AU,C,G */ + 1350 1350 1350 1350 1350 /* UA,AU,C,U */ + 1350 780 1350 780 1350 /* UA,AU,G,N */ + 1350 780 1350 780 1350 /* UA,AU,G,A */ + 1350 780 1350 780 1350 /* UA,AU,G,C */ + 780 780 780 780 780 /* UA,AU,G,G */ + 1350 780 1350 780 1350 /* UA,AU,G,U */ + 1350 1350 1350 1350 340 /* UA,AU,U,N */ + 1350 1350 1350 1350 340 /* UA,AU,U,A */ + 1350 1350 1350 1350 340 /* UA,AU,U,C */ + 1350 1350 1350 1350 340 /* UA,AU,U,G */ + 340 340 340 340 340 /* UA,AU,U,U */ + 1350 1350 1350 1350 1350 /* UA,UA,N,N */ + 1350 1350 1350 1350 1350 /* UA,UA,N,A */ + 1350 1350 1350 1350 1350 /* UA,UA,N,C */ + 1350 1350 1350 1350 1350 /* UA,UA,N,G */ + 1350 1350 1350 1350 1350 /* UA,UA,N,U */ + 1350 1350 1350 780 1350 /* UA,UA,A,N */ + 1350 1350 1350 780 1350 /* UA,UA,A,A */ + 1350 1350 1350 780 1350 /* UA,UA,A,C */ + 780 780 780 780 780 /* UA,UA,A,G */ + 1350 1350 1350 780 1350 /* UA,UA,A,U */ + 1350 1350 1350 1350 1350 /* UA,UA,C,N */ + 1350 1350 1350 1350 1350 /* UA,UA,C,A */ + 1350 1350 1350 1350 1350 /* UA,UA,C,C */ + 1350 1350 1350 1350 1350 /* UA,UA,C,G */ + 1350 1350 1350 1350 1350 /* UA,UA,C,U */ + 1350 780 1350 780 1350 /* UA,UA,G,N */ + 780 780 780 780 780 /* UA,UA,G,A */ + 1350 780 1350 780 1350 /* UA,UA,G,C */ + 780 780 780 780 780 /* UA,UA,G,G */ + 1350 780 1350 780 1350 /* UA,UA,G,U */ + 1350 1350 1350 1350 340 /* UA,UA,U,N */ + 1350 1350 1350 1350 340 /* UA,UA,U,A */ + 1350 1350 1350 1350 340 /* UA,UA,U,C */ + 1350 1350 1350 1350 340 /* UA,UA,U,G */ + 340 340 340 340 340 /* UA,UA,U,U */ + 1350 1350 1350 1350 1350 /* UA,NN,N,N */ + 1350 1350 1350 1350 1350 /* UA,NN,N,A */ + 1350 1350 1350 1350 1350 /* UA,NN,N,C */ + 1350 1350 1350 1350 1350 /* UA,NN,N,G */ + 1350 1350 1350 1350 1350 /* UA,NN,N,U */ + 1350 1350 1350 780 1350 /* UA,NN,A,N */ + 1350 1350 1350 780 1350 /* UA,NN,A,A */ + 1350 1350 1350 780 1350 /* UA,NN,A,C */ + 780 780 780 780 780 /* UA,NN,A,G */ + 1350 1350 1350 780 1350 /* UA,NN,A,U */ + 1350 1350 1350 1350 1350 /* UA,NN,C,N */ + 1350 1350 1350 1350 1350 /* UA,NN,C,A */ + 1350 1350 1350 1350 1350 /* UA,NN,C,C */ + 1350 1350 1350 1350 1350 /* UA,NN,C,G */ + 1350 1350 1350 1350 1350 /* UA,NN,C,U */ + 1350 780 1350 780 1350 /* UA,NN,G,N */ + 1350 780 1350 780 1350 /* UA,NN,G,A */ + 1350 780 1350 780 1350 /* UA,NN,G,C */ + 780 780 780 780 780 /* UA,NN,G,G */ + 1350 780 1350 780 1350 /* UA,NN,G,U */ + 1350 1350 1350 1350 340 /* UA,NN,U,N */ + 1350 1350 1350 1350 340 /* UA,NN,U,A */ + 1350 1350 1350 1350 340 /* UA,NN,U,C */ + 1350 1350 1350 1350 340 /* UA,NN,U,G */ + 340 340 340 340 340 /* UA,NN,U,U */ + 850 850 850 850 850 /* NN,CG,N,N */ + 850 850 850 850 850 /* NN,CG,N,A */ + 850 850 850 850 850 /* NN,CG,N,C */ + 850 850 850 850 850 /* NN,CG,N,G */ + 850 850 850 850 850 /* NN,CG,N,U */ + 850 850 850 850 850 /* NN,CG,A,N */ + 850 850 850 850 850 /* NN,CG,A,A */ + 850 850 850 850 850 /* NN,CG,A,C */ + 280 280 280 280 280 /* NN,CG,A,G */ + 850 850 850 850 850 /* NN,CG,A,U */ + 850 850 850 850 850 /* NN,CG,C,N */ + 850 850 850 850 850 /* NN,CG,C,A */ + 850 850 850 850 850 /* NN,CG,C,C */ + 850 850 850 850 850 /* NN,CG,C,G */ + 850 850 850 850 850 /* NN,CG,C,U */ + 850 280 850 280 850 /* NN,CG,G,N */ + 280 280 280 280 280 /* NN,CG,G,A */ + 850 280 850 280 850 /* NN,CG,G,C */ + 280 280 280 280 280 /* NN,CG,G,G */ + 850 280 850 280 850 /* NN,CG,G,U */ + 850 850 850 850 -160 /* NN,CG,U,N */ + 850 850 850 850 -160 /* NN,CG,U,A */ + 850 850 850 850 -160 /* NN,CG,U,C */ + 850 850 850 850 -160 /* NN,CG,U,G */ + -160 -160 -160 -160 -160 /* NN,CG,U,U */ + 850 850 850 850 850 /* NN,GC,N,N */ + 850 850 850 850 850 /* NN,GC,N,A */ + 850 850 850 850 850 /* NN,GC,N,C */ + 850 850 850 850 850 /* NN,GC,N,G */ + 850 850 850 850 850 /* NN,GC,N,U */ + 850 850 850 850 850 /* NN,GC,A,N */ + 850 850 850 850 850 /* NN,GC,A,A */ + 850 850 850 850 850 /* NN,GC,A,C */ + 280 280 280 280 280 /* NN,GC,A,G */ + 850 850 850 850 850 /* NN,GC,A,U */ + 850 850 850 850 850 /* NN,GC,C,N */ + 850 850 850 850 850 /* NN,GC,C,A */ + 850 850 850 850 850 /* NN,GC,C,C */ + 850 850 850 850 850 /* NN,GC,C,G */ + 850 850 850 850 850 /* NN,GC,C,U */ + 850 280 850 280 850 /* NN,GC,G,N */ + 850 280 850 280 850 /* NN,GC,G,A */ + 850 280 850 280 850 /* NN,GC,G,C */ + 280 280 280 280 280 /* NN,GC,G,G */ + 850 280 850 280 850 /* NN,GC,G,U */ + 850 850 850 850 -160 /* NN,GC,U,N */ + 850 850 850 850 -160 /* NN,GC,U,A */ + 850 850 850 850 -160 /* NN,GC,U,C */ + 850 850 850 850 -160 /* NN,GC,U,G */ + -160 -160 -160 -160 -160 /* NN,GC,U,U */ + 1350 1350 1350 1350 1350 /* NN,GU,N,N */ + 1350 1350 1350 1350 1350 /* NN,GU,N,A */ + 1350 1350 1350 1350 1350 /* NN,GU,N,C */ + 1350 1350 1350 1350 1350 /* NN,GU,N,G */ + 1350 1350 1350 1350 1350 /* NN,GU,N,U */ + 1350 1350 1350 1350 1350 /* NN,GU,A,N */ + 1350 1350 1350 1350 1350 /* NN,GU,A,A */ + 1350 1350 1350 1350 1350 /* NN,GU,A,C */ + 780 780 780 780 780 /* NN,GU,A,G */ + 1350 1350 1350 1350 1350 /* NN,GU,A,U */ + 1350 1350 1350 1350 1350 /* NN,GU,C,N */ + 1350 1350 1350 1350 1350 /* NN,GU,C,A */ + 1350 1350 1350 1350 1350 /* NN,GU,C,C */ + 1350 1350 1350 1350 1350 /* NN,GU,C,G */ + 1350 1350 1350 1350 1350 /* NN,GU,C,U */ + 1350 780 1350 780 1350 /* NN,GU,G,N */ + 1350 780 1350 780 1350 /* NN,GU,G,A */ + 1350 780 1350 780 1350 /* NN,GU,G,C */ + 780 780 780 780 780 /* NN,GU,G,G */ + 1350 780 1350 780 1350 /* NN,GU,G,U */ + 1350 1350 1350 1350 340 /* NN,GU,U,N */ + 1350 1350 1350 1350 340 /* NN,GU,U,A */ + 1350 1350 1350 1350 340 /* NN,GU,U,C */ + 1350 1350 1350 1350 340 /* NN,GU,U,G */ + 340 340 340 340 340 /* NN,GU,U,U */ + 1350 1350 1350 1350 1350 /* NN,UG,N,N */ + 1350 1350 1350 1350 1350 /* NN,UG,N,A */ + 1350 1350 1350 1350 1350 /* NN,UG,N,C */ + 1350 1350 1350 1350 1350 /* NN,UG,N,G */ + 1350 1350 1350 1350 1350 /* NN,UG,N,U */ + 1350 1350 1350 1350 1350 /* NN,UG,A,N */ + 1350 1350 1350 1350 1350 /* NN,UG,A,A */ + 1350 1350 1350 1350 1350 /* NN,UG,A,C */ + 780 780 780 780 780 /* NN,UG,A,G */ + 1350 1350 1350 1350 1350 /* NN,UG,A,U */ + 1350 1350 1350 1350 1350 /* NN,UG,C,N */ + 1350 1350 1350 1350 1350 /* NN,UG,C,A */ + 1350 1350 1350 1350 1350 /* NN,UG,C,C */ + 1350 1350 1350 1350 1350 /* NN,UG,C,G */ + 1350 1350 1350 1350 1350 /* NN,UG,C,U */ + 1350 780 1350 780 1350 /* NN,UG,G,N */ + 780 780 780 780 780 /* NN,UG,G,A */ + 1350 780 1350 780 1350 /* NN,UG,G,C */ + 780 780 780 780 780 /* NN,UG,G,G */ + 1350 780 1350 780 1350 /* NN,UG,G,U */ + 1350 1350 1350 1350 340 /* NN,UG,U,N */ + 1350 1350 1350 1350 340 /* NN,UG,U,A */ + 1350 1350 1350 1350 340 /* NN,UG,U,C */ + 1350 1350 1350 1350 340 /* NN,UG,U,G */ + 340 340 340 340 340 /* NN,UG,U,U */ + 1350 1350 1350 1350 1350 /* NN,AU,N,N */ + 1350 1350 1350 1350 1350 /* NN,AU,N,A */ + 1350 1350 1350 1350 1350 /* NN,AU,N,C */ + 1350 1350 1350 1350 1350 /* NN,AU,N,G */ + 1350 1350 1350 1350 1350 /* NN,AU,N,U */ + 1350 1350 1350 1350 1350 /* NN,AU,A,N */ + 1350 1350 1350 1350 1350 /* NN,AU,A,A */ + 1350 1350 1350 1350 1350 /* NN,AU,A,C */ + 780 780 780 780 780 /* NN,AU,A,G */ + 1350 1350 1350 1350 1350 /* NN,AU,A,U */ + 1350 1350 1350 1350 1350 /* NN,AU,C,N */ + 1350 1350 1350 1350 1350 /* NN,AU,C,A */ + 1350 1350 1350 1350 1350 /* NN,AU,C,C */ + 1350 1350 1350 1350 1350 /* NN,AU,C,G */ + 1350 1350 1350 1350 1350 /* NN,AU,C,U */ + 1350 780 1350 780 1350 /* NN,AU,G,N */ + 1350 780 1350 780 1350 /* NN,AU,G,A */ + 1350 780 1350 780 1350 /* NN,AU,G,C */ + 780 780 780 780 780 /* NN,AU,G,G */ + 1350 780 1350 780 1350 /* NN,AU,G,U */ + 1350 1350 1350 1350 340 /* NN,AU,U,N */ + 1350 1350 1350 1350 340 /* NN,AU,U,A */ + 1350 1350 1350 1350 340 /* NN,AU,U,C */ + 1350 1350 1350 1350 340 /* NN,AU,U,G */ + 340 340 340 340 340 /* NN,AU,U,U */ + 1350 1350 1350 1350 1350 /* NN,UA,N,N */ + 1350 1350 1350 1350 1350 /* NN,UA,N,A */ + 1350 1350 1350 1350 1350 /* NN,UA,N,C */ + 1350 1350 1350 1350 1350 /* NN,UA,N,G */ + 1350 1350 1350 1350 1350 /* NN,UA,N,U */ + 1350 1350 1350 1350 1350 /* NN,UA,A,N */ + 1350 1350 1350 1350 1350 /* NN,UA,A,A */ + 1350 1350 1350 1350 1350 /* NN,UA,A,C */ + 780 780 780 780 780 /* NN,UA,A,G */ + 1350 1350 1350 1350 1350 /* NN,UA,A,U */ + 1350 1350 1350 1350 1350 /* NN,UA,C,N */ + 1350 1350 1350 1350 1350 /* NN,UA,C,A */ + 1350 1350 1350 1350 1350 /* NN,UA,C,C */ + 1350 1350 1350 1350 1350 /* NN,UA,C,G */ + 1350 1350 1350 1350 1350 /* NN,UA,C,U */ + 1350 780 1350 780 1350 /* NN,UA,G,N */ + 780 780 780 780 780 /* NN,UA,G,A */ + 1350 780 1350 780 1350 /* NN,UA,G,C */ + 780 780 780 780 780 /* NN,UA,G,G */ + 1350 780 1350 780 1350 /* NN,UA,G,U */ + 1350 1350 1350 1350 340 /* NN,UA,U,N */ + 1350 1350 1350 1350 340 /* NN,UA,U,A */ + 1350 1350 1350 1350 340 /* NN,UA,U,C */ + 1350 1350 1350 1350 340 /* NN,UA,U,G */ + 340 340 340 340 340 /* NN,UA,U,U */ + 1350 1350 1350 1350 1350 /* NN,NN,N,N */ + 1350 1350 1350 1350 1350 /* NN,NN,N,A */ + 1350 1350 1350 1350 1350 /* NN,NN,N,C */ + 1350 1350 1350 1350 1350 /* NN,NN,N,G */ + 1350 1350 1350 1350 1350 /* NN,NN,N,U */ + 1350 1350 1350 1350 1350 /* NN,NN,A,N */ + 1350 1350 1350 1350 1350 /* NN,NN,A,A */ + 1350 1350 1350 1350 1350 /* NN,NN,A,C */ + 780 780 780 780 780 /* NN,NN,A,G */ + 1350 1350 1350 1350 1350 /* NN,NN,A,U */ + 1350 1350 1350 1350 1350 /* NN,NN,C,N */ + 1350 1350 1350 1350 1350 /* NN,NN,C,A */ + 1350 1350 1350 1350 1350 /* NN,NN,C,C */ + 1350 1350 1350 1350 1350 /* NN,NN,C,G */ + 1350 1350 1350 1350 1350 /* NN,NN,C,U */ + 1350 780 1350 780 1350 /* NN,NN,G,N */ + 1350 780 1350 780 1350 /* NN,NN,G,A */ + 1350 780 1350 780 1350 /* NN,NN,G,C */ + 780 780 780 780 780 /* NN,NN,G,G */ + 1350 780 1350 780 1350 /* NN,NN,G,U */ + 1350 1350 1350 1350 340 /* NN,NN,U,N */ + 1350 1350 1350 1350 340 /* NN,NN,U,A */ + 1350 1350 1350 1350 340 /* NN,NN,U,C */ + 1350 1350 1350 1350 340 /* NN,NN,U,G */ + 340 340 340 340 340 /* NN,NN,U,U */ + +# int22 + 120 160 20 160 /* CG,CG,A,A,A */ + 110 150 20 150 /* CG,CG,A,A,C */ + 20 60 -70 60 /* CG,CG,A,A,G */ + 110 150 20 150 /* CG,CG,A,A,U */ + 160 200 60 200 /* CG,CG,A,C,A */ + 140 180 110 180 /* CG,CG,A,C,C */ + 160 200 60 200 /* CG,CG,A,C,G */ + 130 170 90 170 /* CG,CG,A,C,U */ + 20 60 -70 60 /* CG,CG,A,G,A */ + 110 150 20 150 /* CG,CG,A,G,C */ + -30 10 0 10 /* CG,CG,A,G,G */ + 110 150 20 150 /* CG,CG,A,G,U */ + 160 200 60 200 /* CG,CG,A,U,A */ + 130 170 90 170 /* CG,CG,A,U,C */ + 160 200 60 200 /* CG,CG,A,U,G */ + 100 80 -50 80 /* CG,CG,A,U,U */ + 110 140 110 130 /* CG,CG,C,A,A */ + 110 140 110 120 /* CG,CG,C,A,C */ + 20 110 20 90 /* CG,CG,C,A,G */ + 110 140 110 120 /* CG,CG,C,A,U */ + 150 180 150 170 /* CG,CG,C,C,A */ + 140 170 140 150 /* CG,CG,C,C,C */ + 150 180 150 170 /* CG,CG,C,C,G */ + 120 150 120 140 /* CG,CG,C,C,U */ + 20 110 20 90 /* CG,CG,C,G,A */ + 110 140 110 120 /* CG,CG,C,G,C */ + -40 -10 -40 -20 /* CG,CG,C,G,G */ + 110 140 110 120 /* CG,CG,C,G,U */ + 150 180 150 170 /* CG,CG,C,U,A */ + 120 150 120 140 /* CG,CG,C,U,C */ + 150 180 150 170 /* CG,CG,C,U,G */ + 30 60 30 50 /* CG,CG,C,U,U */ + 20 160 -30 160 /* CG,CG,G,A,A */ + 20 150 -40 150 /* CG,CG,G,A,C */ + -70 60 0 60 /* CG,CG,G,A,G */ + 20 150 -40 150 /* CG,CG,G,A,U */ + 60 200 10 200 /* CG,CG,G,C,A */ + 110 180 -10 180 /* CG,CG,G,C,C */ + 60 200 10 200 /* CG,CG,G,C,G */ + 90 170 -20 170 /* CG,CG,G,C,U */ + -70 60 0 60 /* CG,CG,G,G,A */ + 20 150 -40 150 /* CG,CG,G,G,C */ + 0 10 80 10 /* CG,CG,G,G,G */ + 20 150 -40 150 /* CG,CG,G,G,U */ + 60 200 10 200 /* CG,CG,G,U,A */ + 90 170 -20 170 /* CG,CG,G,U,C */ + 60 200 10 200 /* CG,CG,G,U,G */ + -50 80 20 80 /* CG,CG,G,U,U */ + 110 130 110 100 /* CG,CG,U,A,A */ + 110 120 110 30 /* CG,CG,U,A,C */ + 20 90 20 -50 /* CG,CG,U,A,G */ + 110 120 110 30 /* CG,CG,U,A,U */ + 150 170 150 80 /* CG,CG,U,C,A */ + 140 150 140 60 /* CG,CG,U,C,C */ + 150 170 150 80 /* CG,CG,U,C,G */ + 120 140 120 50 /* CG,CG,U,C,U */ + 20 90 20 -50 /* CG,CG,U,G,A */ + 110 120 110 30 /* CG,CG,U,G,C */ + -40 -20 -40 20 /* CG,CG,U,G,G */ + 110 120 110 30 /* CG,CG,U,G,U */ + 150 170 150 80 /* CG,CG,U,U,A */ + 120 140 120 50 /* CG,CG,U,U,C */ + 150 170 150 80 /* CG,CG,U,U,G */ + 30 50 30 -40 /* CG,CG,U,U,U */ + 130 60 0 170 /* CG,GC,A,A,A */ + 110 150 -70 150 /* CG,GC,A,A,C */ + -30 10 -160 -30 /* CG,GC,A,A,G */ + 110 150 10 150 /* CG,GC,A,A,U */ + 100 50 -100 140 /* CG,GC,A,C,A */ + 110 150 -60 150 /* CG,GC,A,C,C */ + 100 140 10 140 /* CG,GC,A,C,G */ + 110 150 70 150 /* CG,GC,A,C,U */ + 40 30 -70 30 /* CG,GC,A,G,A */ + 110 150 10 150 /* CG,GC,A,G,C */ + -30 -30 0 10 /* CG,GC,A,G,G */ + 110 150 10 150 /* CG,GC,A,G,U */ + 100 140 10 140 /* CG,GC,A,U,A */ + 110 150 80 150 /* CG,GC,A,U,C */ + 100 140 10 140 /* CG,GC,A,U,G */ + 150 0 90 70 /* CG,GC,A,U,U */ + 130 220 130 140 /* CG,GC,C,A,A */ + 100 130 100 120 /* CG,GC,C,A,C */ + -70 70 -70 0 /* CG,GC,C,A,G */ + 100 130 100 120 /* CG,GC,C,A,U */ + 110 190 100 110 /* CG,GC,C,C,A */ + 100 130 100 120 /* CG,GC,C,C,C */ + 100 130 100 110 /* CG,GC,C,C,G */ + 100 130 100 170 /* CG,GC,C,C,U */ + 70 70 -10 60 /* CG,GC,C,G,A */ + 100 130 100 120 /* CG,GC,C,G,C */ + -40 -10 -40 20 /* CG,GC,C,G,G */ + 100 130 100 120 /* CG,GC,C,G,U */ + 100 130 100 110 /* CG,GC,C,U,A */ + 110 140 110 120 /* CG,GC,C,U,C */ + 100 130 100 110 /* CG,GC,C,U,G */ + -20 -10 30 20 /* CG,GC,C,U,U */ + -20 170 -10 170 /* CG,GC,G,A,A */ + -40 150 -40 150 /* CG,GC,G,A,C */ + -170 -30 -90 -30 /* CG,GC,G,A,G */ + 10 150 -40 150 /* CG,GC,G,A,U */ + 70 140 -50 140 /* CG,GC,G,C,A */ + 70 150 -40 150 /* CG,GC,G,C,C */ + 10 140 -50 140 /* CG,GC,G,C,G */ + 70 150 20 150 /* CG,GC,G,C,U */ + -50 30 -30 30 /* CG,GC,G,G,A */ + 10 150 -40 150 /* CG,GC,G,G,C */ + -30 10 80 10 /* CG,GC,G,G,G */ + 10 150 -40 150 /* CG,GC,G,G,U */ + 10 140 -50 140 /* CG,GC,G,U,A */ + 80 150 -50 150 /* CG,GC,G,U,C */ + 10 140 -50 140 /* CG,GC,G,U,G */ + 90 70 140 70 /* CG,GC,G,U,U */ + 130 140 130 140 /* CG,GC,U,A,A */ + 100 120 100 30 /* CG,GC,U,A,C */ + -70 0 -70 50 /* CG,GC,U,A,G */ + 100 120 100 30 /* CG,GC,U,A,U */ + 100 110 100 30 /* CG,GC,U,C,A */ + 100 120 100 30 /* CG,GC,U,C,C */ + 100 110 100 20 /* CG,GC,U,C,G */ + 100 120 100 30 /* CG,GC,U,C,U */ + -10 50 -10 140 /* CG,GC,U,G,A */ + 100 120 100 30 /* CG,GC,U,G,C */ + -40 -60 -40 70 /* CG,GC,U,G,G */ + 100 120 100 30 /* CG,GC,U,G,U */ + 100 110 100 20 /* CG,GC,U,U,A */ + 110 120 110 30 /* CG,GC,U,U,C */ + 100 110 100 20 /* CG,GC,U,U,G */ + 30 40 30 -60 /* CG,GC,U,U,U */ + 270 300 170 300 /* CG,GU,A,A,A */ + 230 270 130 270 /* CG,GU,A,A,C */ + 150 190 50 190 /* CG,GU,A,A,G */ + 230 270 130 270 /* CG,GU,A,A,U */ + 230 270 130 270 /* CG,GU,A,C,A */ + 230 270 190 270 /* CG,GU,A,C,C */ + 230 270 130 270 /* CG,GU,A,C,G */ + 230 270 190 270 /* CG,GU,A,C,U */ + 190 230 90 230 /* CG,GU,A,G,A */ + 230 270 130 270 /* CG,GU,A,G,C */ + 100 140 130 140 /* CG,GU,A,G,G */ + 230 270 130 270 /* CG,GU,A,G,U */ + 230 270 130 270 /* CG,GU,A,U,A */ + 230 270 190 270 /* CG,GU,A,U,C */ + 230 270 130 270 /* CG,GU,A,U,G */ + 290 270 130 270 /* CG,GU,A,U,U */ + 260 290 260 270 /* CG,GU,C,A,A */ + 220 250 220 240 /* CG,GU,C,A,C */ + 140 230 140 220 /* CG,GU,C,A,G */ + 220 250 220 240 /* CG,GU,C,A,U */ + 220 250 220 240 /* CG,GU,C,C,A */ + 220 250 220 240 /* CG,GU,C,C,C */ + 220 250 220 240 /* CG,GU,C,C,G */ + 220 250 220 240 /* CG,GU,C,C,U */ + 180 270 180 260 /* CG,GU,C,G,A */ + 220 250 220 240 /* CG,GU,C,G,C */ + 90 120 90 110 /* CG,GU,C,G,G */ + 220 250 220 240 /* CG,GU,C,G,U */ + 220 250 220 240 /* CG,GU,C,U,A */ + 220 250 220 240 /* CG,GU,C,U,C */ + 220 250 220 240 /* CG,GU,C,U,G */ + 220 250 220 240 /* CG,GU,C,U,U */ + 170 300 110 300 /* CG,GU,G,A,A */ + 130 270 80 270 /* CG,GU,G,A,C */ + 50 190 130 190 /* CG,GU,G,A,G */ + 130 270 80 270 /* CG,GU,G,A,U */ + 130 270 80 270 /* CG,GU,G,C,A */ + 190 270 80 270 /* CG,GU,G,C,C */ + 130 270 80 270 /* CG,GU,G,C,G */ + 190 270 80 270 /* CG,GU,G,C,U */ + 90 230 170 230 /* CG,GU,G,G,A */ + 130 270 80 270 /* CG,GU,G,G,C */ + 130 140 210 140 /* CG,GU,G,G,G */ + 130 270 80 270 /* CG,GU,G,G,U */ + 130 270 80 270 /* CG,GU,G,U,A */ + 190 270 80 270 /* CG,GU,G,U,C */ + 130 270 80 270 /* CG,GU,G,U,G */ + 130 270 210 270 /* CG,GU,G,U,U */ + 260 270 260 240 /* CG,GU,U,A,A */ + 220 240 220 150 /* CG,GU,U,A,C */ + 140 220 140 70 /* CG,GU,U,A,G */ + 220 240 220 150 /* CG,GU,U,A,U */ + 220 240 220 150 /* CG,GU,U,C,A */ + 220 240 220 150 /* CG,GU,U,C,C */ + 220 240 220 150 /* CG,GU,U,C,G */ + 220 240 220 150 /* CG,GU,U,C,U */ + 180 260 180 110 /* CG,GU,U,G,A */ + 220 240 220 150 /* CG,GU,U,G,C */ + 90 110 90 150 /* CG,GU,U,G,G */ + 220 240 220 150 /* CG,GU,U,G,U */ + 220 240 220 150 /* CG,GU,U,U,A */ + 220 240 220 150 /* CG,GU,U,U,C */ + 220 240 220 150 /* CG,GU,U,U,G */ + 220 240 220 150 /* CG,GU,U,U,U */ + 160 200 70 200 /* CG,UG,A,A,A */ + 200 240 100 240 /* CG,UG,A,A,C */ + 60 100 -30 100 /* CG,UG,A,A,G */ + 200 240 100 240 /* CG,UG,A,A,U */ + 200 240 100 240 /* CG,UG,A,C,A */ + 200 240 160 240 /* CG,UG,A,C,C */ + 200 240 100 240 /* CG,UG,A,C,G */ + 200 240 160 240 /* CG,UG,A,C,U */ + 230 270 130 270 /* CG,UG,A,G,A */ + 200 240 100 240 /* CG,UG,A,G,C */ + 70 110 100 110 /* CG,UG,A,G,G */ + 200 240 100 240 /* CG,UG,A,G,U */ + 200 240 100 240 /* CG,UG,A,U,A */ + 200 240 160 240 /* CG,UG,A,U,C */ + 200 240 100 240 /* CG,UG,A,U,G */ + 260 240 100 240 /* CG,UG,A,U,U */ + 160 190 160 170 /* CG,UG,C,A,A */ + 190 220 190 210 /* CG,UG,C,A,C */ + 60 150 60 130 /* CG,UG,C,A,G */ + 190 220 190 210 /* CG,UG,C,A,U */ + 190 220 190 210 /* CG,UG,C,C,A */ + 190 220 190 210 /* CG,UG,C,C,C */ + 190 220 190 210 /* CG,UG,C,C,G */ + 190 220 190 210 /* CG,UG,C,C,U */ + 220 310 220 300 /* CG,UG,C,G,A */ + 190 220 190 210 /* CG,UG,C,G,C */ + 60 90 60 80 /* CG,UG,C,G,G */ + 190 220 190 210 /* CG,UG,C,G,U */ + 190 220 190 210 /* CG,UG,C,U,A */ + 190 220 190 210 /* CG,UG,C,U,C */ + 190 220 190 210 /* CG,UG,C,U,G */ + 190 220 190 210 /* CG,UG,C,U,U */ + 70 200 10 200 /* CG,UG,G,A,A */ + 100 240 50 240 /* CG,UG,G,A,C */ + -30 100 40 100 /* CG,UG,G,A,G */ + 100 240 50 240 /* CG,UG,G,A,U */ + 100 240 50 240 /* CG,UG,G,C,A */ + 160 240 50 240 /* CG,UG,G,C,C */ + 100 240 50 240 /* CG,UG,G,C,G */ + 160 240 50 240 /* CG,UG,G,C,U */ + 130 270 210 270 /* CG,UG,G,G,A */ + 100 240 50 240 /* CG,UG,G,G,C */ + 100 110 180 110 /* CG,UG,G,G,G */ + 100 240 50 240 /* CG,UG,G,G,U */ + 100 240 50 240 /* CG,UG,G,U,A */ + 160 240 50 240 /* CG,UG,G,U,C */ + 100 240 50 240 /* CG,UG,G,U,G */ + 100 240 180 240 /* CG,UG,G,U,U */ + 160 170 160 140 /* CG,UG,U,A,A */ + 190 210 190 120 /* CG,UG,U,A,C */ + 60 130 60 -10 /* CG,UG,U,A,G */ + 190 210 190 120 /* CG,UG,U,A,U */ + 190 210 190 120 /* CG,UG,U,C,A */ + 190 210 190 120 /* CG,UG,U,C,C */ + 190 210 190 120 /* CG,UG,U,C,G */ + 190 210 190 120 /* CG,UG,U,C,U */ + 220 300 220 150 /* CG,UG,U,G,A */ + 190 210 190 120 /* CG,UG,U,G,C */ + 60 80 60 120 /* CG,UG,U,G,G */ + 190 210 190 120 /* CG,UG,U,G,U */ + 190 210 190 120 /* CG,UG,U,U,A */ + 190 210 190 120 /* CG,UG,U,U,C */ + 190 210 190 120 /* CG,UG,U,U,G */ + 190 210 190 120 /* CG,UG,U,U,U */ + 200 240 100 240 /* CG,AU,A,A,A */ + 170 210 80 210 /* CG,AU,A,A,C */ + 70 110 -20 110 /* CG,AU,A,A,G */ + 170 210 80 210 /* CG,AU,A,A,U */ + 180 220 90 220 /* CG,AU,A,C,A */ + 180 220 140 220 /* CG,AU,A,C,C */ + 180 220 90 220 /* CG,AU,A,C,G */ + 180 220 140 220 /* CG,AU,A,C,U */ + 140 180 50 180 /* CG,AU,A,G,A */ + 170 210 80 210 /* CG,AU,A,G,C */ + 20 60 60 60 /* CG,AU,A,G,G */ + 170 210 80 210 /* CG,AU,A,G,U */ + 180 220 90 220 /* CG,AU,A,U,A */ + 180 220 140 220 /* CG,AU,A,U,C */ + 180 220 90 220 /* CG,AU,A,U,G */ + 150 130 0 130 /* CG,AU,A,U,U */ + 190 220 190 210 /* CG,AU,C,A,A */ + 170 200 170 180 /* CG,AU,C,A,C */ + 70 160 70 140 /* CG,AU,C,A,G */ + 170 200 170 180 /* CG,AU,C,A,U */ + 180 210 180 190 /* CG,AU,C,C,A */ + 170 200 170 190 /* CG,AU,C,C,C */ + 180 210 180 190 /* CG,AU,C,C,G */ + 170 200 170 190 /* CG,AU,C,C,U */ + 140 230 140 210 /* CG,AU,C,G,A */ + 170 200 170 180 /* CG,AU,C,G,C */ + 20 50 20 30 /* CG,AU,C,G,G */ + 170 200 170 180 /* CG,AU,C,G,U */ + 180 210 180 190 /* CG,AU,C,U,A */ + 170 200 170 190 /* CG,AU,C,U,C */ + 180 210 180 190 /* CG,AU,C,U,G */ + 80 110 80 100 /* CG,AU,C,U,U */ + 100 240 50 240 /* CG,AU,G,A,A */ + 80 210 20 210 /* CG,AU,G,A,C */ + -20 110 50 110 /* CG,AU,G,A,G */ + 80 210 20 210 /* CG,AU,G,A,U */ + 90 220 30 220 /* CG,AU,G,C,A */ + 140 220 30 220 /* CG,AU,G,C,C */ + 90 220 30 220 /* CG,AU,G,C,G */ + 140 220 30 220 /* CG,AU,G,C,U */ + 50 180 120 180 /* CG,AU,G,G,A */ + 80 210 20 210 /* CG,AU,G,G,C */ + 60 60 130 60 /* CG,AU,G,G,G */ + 80 210 20 210 /* CG,AU,G,G,U */ + 90 220 30 220 /* CG,AU,G,U,A */ + 140 220 30 220 /* CG,AU,G,U,C */ + 90 220 30 220 /* CG,AU,G,U,G */ + 0 130 70 130 /* CG,AU,G,U,U */ + 190 210 190 180 /* CG,AU,U,A,A */ + 170 180 170 90 /* CG,AU,U,A,C */ + 70 140 70 0 /* CG,AU,U,A,G */ + 170 180 170 90 /* CG,AU,U,A,U */ + 180 190 180 100 /* CG,AU,U,C,A */ + 170 190 170 100 /* CG,AU,U,C,C */ + 180 190 180 100 /* CG,AU,U,C,G */ + 170 190 170 100 /* CG,AU,U,C,U */ + 140 210 140 60 /* CG,AU,U,G,A */ + 170 180 170 90 /* CG,AU,U,G,C */ + 20 30 20 70 /* CG,AU,U,G,G */ + 170 180 170 90 /* CG,AU,U,G,U */ + 180 190 180 100 /* CG,AU,U,U,A */ + 170 190 170 100 /* CG,AU,U,U,C */ + 180 190 180 100 /* CG,AU,U,U,G */ + 80 100 80 10 /* CG,AU,U,U,U */ + 200 240 100 240 /* CG,UA,A,A,A */ + 150 190 60 190 /* CG,UA,A,A,C */ + 90 130 0 130 /* CG,UA,A,A,G */ + 150 190 60 190 /* CG,UA,A,A,U */ + 200 240 100 240 /* CG,UA,A,C,A */ + 200 240 160 240 /* CG,UA,A,C,C */ + 200 240 100 240 /* CG,UA,A,C,G */ + 200 240 160 240 /* CG,UA,A,C,U */ + 100 140 10 140 /* CG,UA,A,G,A */ + 150 190 60 190 /* CG,UA,A,G,C */ + 40 80 80 80 /* CG,UA,A,G,G */ + 150 190 60 190 /* CG,UA,A,G,U */ + 200 240 100 240 /* CG,UA,A,U,A */ + 170 210 130 210 /* CG,UA,A,U,C */ + 200 240 100 240 /* CG,UA,A,U,G */ + 170 150 20 150 /* CG,UA,A,U,U */ + 190 220 190 210 /* CG,UA,C,A,A */ + 150 180 150 160 /* CG,UA,C,A,C */ + 90 180 90 160 /* CG,UA,C,A,G */ + 150 180 150 160 /* CG,UA,C,A,U */ + 190 220 190 210 /* CG,UA,C,C,A */ + 190 220 190 210 /* CG,UA,C,C,C */ + 190 220 190 210 /* CG,UA,C,C,G */ + 190 220 190 210 /* CG,UA,C,C,U */ + 100 190 100 170 /* CG,UA,C,G,A */ + 150 180 150 160 /* CG,UA,C,G,C */ + 40 70 40 50 /* CG,UA,C,G,G */ + 150 180 150 160 /* CG,UA,C,G,U */ + 190 220 190 210 /* CG,UA,C,U,A */ + 160 190 160 180 /* CG,UA,C,U,C */ + 190 220 190 210 /* CG,UA,C,U,G */ + 110 140 110 120 /* CG,UA,C,U,U */ + 100 240 50 240 /* CG,UA,G,A,A */ + 60 190 0 190 /* CG,UA,G,A,C */ + 0 130 70 130 /* CG,UA,G,A,G */ + 60 190 0 190 /* CG,UA,G,A,U */ + 100 240 50 240 /* CG,UA,G,C,A */ + 160 240 50 240 /* CG,UA,G,C,C */ + 100 240 50 240 /* CG,UA,G,C,G */ + 160 240 50 240 /* CG,UA,G,C,U */ + 10 140 80 140 /* CG,UA,G,G,A */ + 60 190 0 190 /* CG,UA,G,G,C */ + 80 80 150 80 /* CG,UA,G,G,G */ + 60 190 0 190 /* CG,UA,G,G,U */ + 100 240 50 240 /* CG,UA,G,U,A */ + 130 210 20 210 /* CG,UA,G,U,C */ + 100 240 50 240 /* CG,UA,G,U,G */ + 20 150 90 150 /* CG,UA,G,U,U */ + 190 210 190 180 /* CG,UA,U,A,A */ + 150 160 150 70 /* CG,UA,U,A,C */ + 90 160 90 10 /* CG,UA,U,A,G */ + 150 160 150 70 /* CG,UA,U,A,U */ + 190 210 190 120 /* CG,UA,U,C,A */ + 190 210 190 120 /* CG,UA,U,C,C */ + 190 210 190 120 /* CG,UA,U,C,G */ + 190 210 190 120 /* CG,UA,U,C,U */ + 100 170 100 20 /* CG,UA,U,G,A */ + 150 160 150 70 /* CG,UA,U,G,C */ + 40 50 40 90 /* CG,UA,U,G,G */ + 150 160 150 70 /* CG,UA,U,G,U */ + 190 210 190 120 /* CG,UA,U,U,A */ + 160 180 160 90 /* CG,UA,U,U,C */ + 190 210 190 120 /* CG,UA,U,U,G */ + 110 120 110 30 /* CG,UA,U,U,U */ + 130 100 40 100 /* GC,CG,A,A,A */ + 130 110 70 100 /* GC,CG,A,A,C */ + -20 70 -50 10 /* GC,CG,A,A,G */ + 130 100 -10 100 /* GC,CG,A,A,U */ + 60 50 30 140 /* GC,CG,A,C,A */ + 220 190 70 130 /* GC,CG,A,C,C */ + 170 140 30 140 /* GC,CG,A,C,G */ + 140 110 50 110 /* GC,CG,A,C,U */ + 0 -100 -70 10 /* GC,CG,A,G,A */ + 130 100 -10 100 /* GC,CG,A,G,C */ + -10 -50 -30 -50 /* GC,CG,A,G,G */ + 130 100 -10 100 /* GC,CG,A,G,U */ + 170 140 30 140 /* GC,CG,A,U,A */ + 140 110 60 110 /* GC,CG,A,U,C */ + 170 140 30 140 /* GC,CG,A,U,G */ + 140 30 140 20 /* GC,CG,A,U,U */ + 110 110 110 110 /* GC,CG,C,A,A */ + 100 100 100 110 /* GC,CG,C,A,C */ + -40 70 10 80 /* GC,CG,C,A,G */ + 100 100 100 110 /* GC,CG,C,A,U */ + 150 150 150 150 /* GC,CG,C,C,A */ + 130 130 130 140 /* GC,CG,C,C,C */ + 150 150 150 150 /* GC,CG,C,C,G */ + 120 120 120 120 /* GC,CG,C,C,U */ + -70 -60 10 80 /* GC,CG,C,G,A */ + 100 100 100 110 /* GC,CG,C,G,C */ + -40 -40 -40 -50 /* GC,CG,C,G,G */ + 100 100 100 110 /* GC,CG,C,G,U */ + 150 150 150 150 /* GC,CG,C,U,A */ + 120 120 120 120 /* GC,CG,C,U,C */ + 150 150 150 150 /* GC,CG,C,U,G */ + 30 30 30 30 /* GC,CG,C,U,U */ + -30 100 -30 100 /* GC,CG,G,A,A */ + -70 100 -40 100 /* GC,CG,G,A,C */ + -170 10 -30 10 /* GC,CG,G,A,G */ + -70 100 -40 100 /* GC,CG,G,A,U */ + 10 140 -30 140 /* GC,CG,G,C,A */ + 70 130 -10 130 /* GC,CG,G,C,C */ + -30 140 10 140 /* GC,CG,G,C,G */ + 0 110 -60 110 /* GC,CG,G,C,U */ + -160 10 0 10 /* GC,CG,G,G,A */ + -70 100 -40 100 /* GC,CG,G,G,C */ + -90 -50 80 -50 /* GC,CG,G,G,G */ + -70 100 -40 100 /* GC,CG,G,G,U */ + -30 140 10 140 /* GC,CG,G,U,A */ + 0 110 20 110 /* GC,CG,G,U,C */ + -30 140 10 140 /* GC,CG,G,U,G */ + 50 20 70 20 /* GC,CG,G,U,U */ + 110 110 110 150 /* GC,CG,U,A,A */ + 100 100 100 -20 /* GC,CG,U,A,C */ + 10 70 10 90 /* GC,CG,U,A,G */ + 100 100 100 30 /* GC,CG,U,A,U */ + 150 150 150 0 /* GC,CG,U,C,A */ + 130 130 130 -10 /* GC,CG,U,C,C */ + 150 150 150 70 /* GC,CG,U,C,G */ + 120 120 120 40 /* GC,CG,U,C,U */ + 10 70 10 90 /* GC,CG,U,G,A */ + 100 100 100 30 /* GC,CG,U,G,C */ + -40 20 -40 140 /* GC,CG,U,G,G */ + 100 100 100 30 /* GC,CG,U,G,U */ + 150 150 150 70 /* GC,CG,U,U,A */ + 120 170 120 20 /* GC,CG,U,U,C */ + 150 150 150 70 /* GC,CG,U,U,G */ + 30 30 30 -60 /* GC,CG,U,U,U */ + 150 120 10 120 /* GC,GC,A,A,A */ + 120 90 -10 90 /* GC,GC,A,A,C */ + -50 -80 -190 -80 /* GC,GC,A,A,G */ + 120 90 -10 90 /* GC,GC,A,A,U */ + 120 90 -20 90 /* GC,GC,A,C,A */ + 120 90 50 90 /* GC,GC,A,C,C */ + 120 90 -20 90 /* GC,GC,A,C,G */ + 120 90 50 90 /* GC,GC,A,C,U */ + 10 -20 -130 -20 /* GC,GC,A,G,A */ + 120 90 -10 90 /* GC,GC,A,G,C */ + -20 -50 -20 -50 /* GC,GC,A,G,G */ + 120 90 -10 90 /* GC,GC,A,G,U */ + 120 90 -20 90 /* GC,GC,A,U,A */ + 130 100 50 100 /* GC,GC,A,U,C */ + 120 90 -20 90 /* GC,GC,A,U,G */ + 110 20 -90 20 /* GC,GC,A,U,U */ + 120 120 120 130 /* GC,GC,C,A,A */ + 100 100 100 100 /* GC,GC,C,A,C */ + -80 -20 -80 -10 /* GC,GC,C,A,G */ + 100 100 100 100 /* GC,GC,C,A,U */ + 90 90 90 100 /* GC,GC,C,C,A */ + 100 100 100 100 /* GC,GC,C,C,C */ + 90 90 90 100 /* GC,GC,C,C,G */ + 100 100 100 100 /* GC,GC,C,C,U */ + -10 50 -10 50 /* GC,GC,C,G,A */ + 100 100 100 100 /* GC,GC,C,G,C */ + -40 -40 -40 -40 /* GC,GC,C,G,G */ + 100 100 100 100 /* GC,GC,C,G,U */ + 90 90 90 100 /* GC,GC,C,U,A */ + 100 100 100 110 /* GC,GC,C,U,C */ + 90 90 90 100 /* GC,GC,C,U,G */ + 20 20 20 30 /* GC,GC,C,U,U */ + -50 120 -20 120 /* GC,GC,G,A,A */ + -80 90 -40 90 /* GC,GC,G,A,C */ + -260 -80 -90 -80 /* GC,GC,G,A,G */ + -80 90 -40 90 /* GC,GC,G,A,U */ + -80 90 -50 90 /* GC,GC,G,C,A */ + -20 90 -40 90 /* GC,GC,G,C,C */ + -80 90 -50 90 /* GC,GC,G,C,G */ + -20 90 -40 90 /* GC,GC,G,C,U */ + -190 -20 -20 -20 /* GC,GC,G,G,A */ + -80 90 -40 90 /* GC,GC,G,G,C */ + -90 -50 80 -50 /* GC,GC,G,G,G */ + -80 90 -40 90 /* GC,GC,G,G,U */ + -80 90 -50 90 /* GC,GC,G,U,A */ + -10 100 -40 100 /* GC,GC,G,U,C */ + -80 90 -50 90 /* GC,GC,G,U,G */ + -150 20 10 20 /* GC,GC,G,U,U */ + 120 120 120 110 /* GC,GC,U,A,A */ + 100 100 100 20 /* GC,GC,U,A,C */ + -80 -20 -80 -150 /* GC,GC,U,A,G */ + 100 100 100 20 /* GC,GC,U,A,U */ + 90 90 90 20 /* GC,GC,U,C,A */ + 100 100 100 20 /* GC,GC,U,C,C */ + 90 90 90 20 /* GC,GC,U,C,G */ + 100 100 100 20 /* GC,GC,U,C,U */ + -10 50 -10 -90 /* GC,GC,U,G,A */ + 100 100 100 20 /* GC,GC,U,G,C */ + -40 -40 -40 10 /* GC,GC,U,G,G */ + 100 100 100 20 /* GC,GC,U,G,U */ + 90 90 90 20 /* GC,GC,U,U,A */ + 100 100 100 30 /* GC,GC,U,U,C */ + 90 90 90 20 /* GC,GC,U,U,G */ + 20 20 20 -50 /* GC,GC,U,U,U */ + 280 250 140 250 /* GC,GU,A,A,A */ + 240 210 100 210 /* GC,GU,A,A,C */ + 160 130 20 130 /* GC,GU,A,A,G */ + 240 210 100 210 /* GC,GU,A,A,U */ + 240 210 100 210 /* GC,GU,A,C,A */ + 240 210 160 210 /* GC,GU,A,C,C */ + 240 210 100 210 /* GC,GU,A,C,G */ + 240 210 160 210 /* GC,GU,A,C,U */ + 200 170 60 170 /* GC,GU,A,G,A */ + 240 210 100 210 /* GC,GU,A,G,C */ + 110 80 100 80 /* GC,GU,A,G,G */ + 240 210 100 210 /* GC,GU,A,G,U */ + 240 210 100 210 /* GC,GU,A,U,A */ + 240 210 160 210 /* GC,GU,A,U,C */ + 240 210 100 210 /* GC,GU,A,U,G */ + 300 210 100 210 /* GC,GU,A,U,U */ + 250 250 250 260 /* GC,GU,C,A,A */ + 220 220 220 220 /* GC,GU,C,A,C */ + 140 200 140 200 /* GC,GU,C,A,G */ + 220 220 220 220 /* GC,GU,C,A,U */ + 220 220 220 220 /* GC,GU,C,C,A */ + 220 220 220 220 /* GC,GU,C,C,C */ + 220 220 220 220 /* GC,GU,C,C,G */ + 220 220 220 220 /* GC,GU,C,C,U */ + 180 240 180 240 /* GC,GU,C,G,A */ + 220 220 220 220 /* GC,GU,C,G,C */ + 90 90 90 90 /* GC,GU,C,G,G */ + 220 220 220 220 /* GC,GU,C,G,U */ + 220 220 220 220 /* GC,GU,C,U,A */ + 220 220 220 220 /* GC,GU,C,U,C */ + 220 220 220 220 /* GC,GU,C,U,G */ + 220 220 220 220 /* GC,GU,C,U,U */ + 70 250 110 250 /* GC,GU,G,A,A */ + 40 210 80 210 /* GC,GU,G,A,C */ + -40 130 130 130 /* GC,GU,G,A,G */ + 40 210 80 210 /* GC,GU,G,A,U */ + 40 210 80 210 /* GC,GU,G,C,A */ + 100 210 80 210 /* GC,GU,G,C,C */ + 40 210 80 210 /* GC,GU,G,C,G */ + 100 210 80 210 /* GC,GU,G,C,U */ + 0 170 170 170 /* GC,GU,G,G,A */ + 40 210 80 210 /* GC,GU,G,G,C */ + 40 80 210 80 /* GC,GU,G,G,G */ + 40 210 80 210 /* GC,GU,G,G,U */ + 40 210 80 210 /* GC,GU,G,U,A */ + 100 210 80 210 /* GC,GU,G,U,C */ + 40 210 80 210 /* GC,GU,G,U,G */ + 40 210 210 210 /* GC,GU,G,U,U */ + 250 250 250 240 /* GC,GU,U,A,A */ + 220 220 220 140 /* GC,GU,U,A,C */ + 140 200 140 60 /* GC,GU,U,A,G */ + 220 220 220 140 /* GC,GU,U,A,U */ + 220 220 220 140 /* GC,GU,U,C,A */ + 220 220 220 140 /* GC,GU,U,C,C */ + 220 220 220 140 /* GC,GU,U,C,G */ + 220 220 220 140 /* GC,GU,U,C,U */ + 180 240 180 100 /* GC,GU,U,G,A */ + 220 220 220 140 /* GC,GU,U,G,C */ + 90 90 90 140 /* GC,GU,U,G,G */ + 220 220 220 140 /* GC,GU,U,G,U */ + 220 220 220 140 /* GC,GU,U,U,A */ + 220 220 220 140 /* GC,GU,U,U,C */ + 220 220 220 140 /* GC,GU,U,U,G */ + 220 220 220 140 /* GC,GU,U,U,U */ + 190 150 40 150 /* GC,UG,A,A,A */ + 210 180 70 180 /* GC,UG,A,A,C */ + 80 50 -60 50 /* GC,UG,A,A,G */ + 210 180 70 180 /* GC,UG,A,A,U */ + 210 180 70 180 /* GC,UG,A,C,A */ + 210 180 130 180 /* GC,UG,A,C,C */ + 210 180 70 180 /* GC,UG,A,C,G */ + 210 180 130 180 /* GC,UG,A,C,U */ + 240 210 100 210 /* GC,UG,A,G,A */ + 210 180 70 180 /* GC,UG,A,G,C */ + 80 50 70 50 /* GC,UG,A,G,G */ + 210 180 70 180 /* GC,UG,A,G,U */ + 210 180 70 180 /* GC,UG,A,U,A */ + 210 180 130 180 /* GC,UG,A,U,C */ + 210 180 70 180 /* GC,UG,A,U,G */ + 270 180 70 180 /* GC,UG,A,U,U */ + 150 150 150 160 /* GC,UG,C,A,A */ + 190 190 190 190 /* GC,UG,C,A,C */ + 50 110 50 120 /* GC,UG,C,A,G */ + 190 190 190 190 /* GC,UG,C,A,U */ + 190 190 190 190 /* GC,UG,C,C,A */ + 190 190 190 190 /* GC,UG,C,C,C */ + 190 190 190 190 /* GC,UG,C,C,G */ + 190 190 190 190 /* GC,UG,C,C,U */ + 220 280 220 280 /* GC,UG,C,G,A */ + 190 190 190 190 /* GC,UG,C,G,C */ + 60 60 60 60 /* GC,UG,C,G,G */ + 190 190 190 190 /* GC,UG,C,G,U */ + 190 190 190 190 /* GC,UG,C,U,A */ + 190 190 190 190 /* GC,UG,C,U,C */ + 190 190 190 190 /* GC,UG,C,U,G */ + 190 190 190 190 /* GC,UG,C,U,U */ + -20 150 10 150 /* GC,UG,G,A,A */ + 10 180 50 180 /* GC,UG,G,A,C */ + -120 50 40 50 /* GC,UG,G,A,G */ + 10 180 50 180 /* GC,UG,G,A,U */ + 10 180 50 180 /* GC,UG,G,C,A */ + 70 180 50 180 /* GC,UG,G,C,C */ + 10 180 50 180 /* GC,UG,G,C,G */ + 70 180 50 180 /* GC,UG,G,C,U */ + 40 210 210 210 /* GC,UG,G,G,A */ + 10 180 50 180 /* GC,UG,G,G,C */ + 10 50 180 50 /* GC,UG,G,G,G */ + 10 180 50 180 /* GC,UG,G,G,U */ + 10 180 50 180 /* GC,UG,G,U,A */ + 70 180 50 180 /* GC,UG,G,U,C */ + 10 180 50 180 /* GC,UG,G,U,G */ + 10 180 180 180 /* GC,UG,G,U,U */ + 150 150 150 140 /* GC,UG,U,A,A */ + 190 190 190 110 /* GC,UG,U,A,C */ + 50 110 50 -20 /* GC,UG,U,A,G */ + 190 190 190 110 /* GC,UG,U,A,U */ + 190 190 190 110 /* GC,UG,U,C,A */ + 190 190 190 110 /* GC,UG,U,C,C */ + 190 190 190 110 /* GC,UG,U,C,G */ + 190 190 190 110 /* GC,UG,U,C,U */ + 220 280 220 140 /* GC,UG,U,G,A */ + 190 190 190 110 /* GC,UG,U,G,C */ + 60 60 60 110 /* GC,UG,U,G,G */ + 190 190 190 110 /* GC,UG,U,G,U */ + 190 190 190 110 /* GC,UG,U,U,A */ + 190 190 190 110 /* GC,UG,U,U,C */ + 190 190 190 110 /* GC,UG,U,U,G */ + 190 190 190 110 /* GC,UG,U,U,U */ + 210 180 70 180 /* GC,AU,A,A,A */ + 190 160 50 160 /* GC,AU,A,A,C */ + 90 60 -50 60 /* GC,AU,A,A,G */ + 190 160 50 160 /* GC,AU,A,A,U */ + 200 170 60 170 /* GC,AU,A,C,A */ + 190 160 110 160 /* GC,AU,A,C,C */ + 200 170 60 170 /* GC,AU,A,C,G */ + 190 160 110 160 /* GC,AU,A,C,U */ + 160 130 20 130 /* GC,AU,A,G,A */ + 190 160 50 160 /* GC,AU,A,G,C */ + 40 10 30 10 /* GC,AU,A,G,G */ + 190 160 50 160 /* GC,AU,A,G,U */ + 200 170 60 170 /* GC,AU,A,U,A */ + 190 160 110 160 /* GC,AU,A,U,C */ + 200 170 60 170 /* GC,AU,A,U,G */ + 160 70 -30 70 /* GC,AU,A,U,U */ + 190 190 190 190 /* GC,AU,C,A,A */ + 160 160 160 170 /* GC,AU,C,A,C */ + 60 120 60 130 /* GC,AU,C,A,G */ + 160 160 160 170 /* GC,AU,C,A,U */ + 170 170 170 180 /* GC,AU,C,C,A */ + 170 170 170 170 /* GC,AU,C,C,C */ + 170 170 170 180 /* GC,AU,C,C,G */ + 170 170 170 170 /* GC,AU,C,C,U */ + 130 190 130 200 /* GC,AU,C,G,A */ + 160 160 160 170 /* GC,AU,C,G,C */ + 10 10 10 20 /* GC,AU,C,G,G */ + 160 160 160 170 /* GC,AU,C,G,U */ + 170 170 170 180 /* GC,AU,C,U,A */ + 170 170 170 170 /* GC,AU,C,U,C */ + 170 170 170 180 /* GC,AU,C,U,G */ + 80 80 80 80 /* GC,AU,C,U,U */ + 10 180 50 180 /* GC,AU,G,A,A */ + -10 160 20 160 /* GC,AU,G,A,C */ + -110 60 50 60 /* GC,AU,G,A,G */ + -10 160 20 160 /* GC,AU,G,A,U */ + 0 170 30 170 /* GC,AU,G,C,A */ + 50 160 30 160 /* GC,AU,G,C,C */ + 0 170 30 170 /* GC,AU,G,C,G */ + 50 160 30 160 /* GC,AU,G,C,U */ + -40 130 120 130 /* GC,AU,G,G,A */ + -10 160 20 160 /* GC,AU,G,G,C */ + -30 10 130 10 /* GC,AU,G,G,G */ + -10 160 20 160 /* GC,AU,G,G,U */ + 0 170 30 170 /* GC,AU,G,U,A */ + 50 160 30 160 /* GC,AU,G,U,C */ + 0 170 30 170 /* GC,AU,G,U,G */ + -100 70 70 70 /* GC,AU,G,U,U */ + 190 190 190 170 /* GC,AU,U,A,A */ + 160 160 160 90 /* GC,AU,U,A,C */ + 60 120 60 -10 /* GC,AU,U,A,G */ + 160 160 160 90 /* GC,AU,U,A,U */ + 170 170 170 100 /* GC,AU,U,C,A */ + 170 170 170 90 /* GC,AU,U,C,C */ + 170 170 170 100 /* GC,AU,U,C,G */ + 170 170 170 90 /* GC,AU,U,C,U */ + 130 190 130 60 /* GC,AU,U,G,A */ + 160 160 160 90 /* GC,AU,U,G,C */ + 10 10 10 70 /* GC,AU,U,G,G */ + 160 160 160 90 /* GC,AU,U,G,U */ + 170 170 170 100 /* GC,AU,U,U,A */ + 170 170 170 90 /* GC,AU,U,U,C */ + 170 170 170 100 /* GC,AU,U,U,G */ + 80 80 80 0 /* GC,AU,U,U,U */ + 210 180 70 180 /* GC,UA,A,A,A */ + 170 140 30 140 /* GC,UA,A,A,C */ + 110 80 -30 80 /* GC,UA,A,A,G */ + 170 140 30 140 /* GC,UA,A,A,U */ + 210 180 70 180 /* GC,UA,A,C,A */ + 210 180 130 180 /* GC,UA,A,C,C */ + 210 180 70 180 /* GC,UA,A,C,G */ + 210 180 130 180 /* GC,UA,A,C,U */ + 120 90 -20 90 /* GC,UA,A,G,A */ + 170 140 30 140 /* GC,UA,A,G,C */ + 60 30 50 30 /* GC,UA,A,G,G */ + 170 140 30 140 /* GC,UA,A,G,U */ + 210 180 70 180 /* GC,UA,A,U,A */ + 180 150 100 150 /* GC,UA,A,U,C */ + 210 180 70 180 /* GC,UA,A,U,G */ + 190 100 -10 100 /* GC,UA,A,U,U */ + 190 190 190 190 /* GC,UA,C,A,A */ + 140 140 140 150 /* GC,UA,C,A,C */ + 80 140 80 150 /* GC,UA,C,A,G */ + 140 140 140 150 /* GC,UA,C,A,U */ + 190 190 190 190 /* GC,UA,C,C,A */ + 190 190 190 190 /* GC,UA,C,C,C */ + 190 190 190 190 /* GC,UA,C,C,G */ + 190 190 190 190 /* GC,UA,C,C,U */ + 90 150 90 160 /* GC,UA,C,G,A */ + 140 140 140 150 /* GC,UA,C,G,C */ + 30 30 30 40 /* GC,UA,C,G,G */ + 140 140 140 150 /* GC,UA,C,G,U */ + 190 190 190 190 /* GC,UA,C,U,A */ + 160 160 160 160 /* GC,UA,C,U,C */ + 190 190 190 190 /* GC,UA,C,U,G */ + 100 100 100 110 /* GC,UA,C,U,U */ + 10 180 50 180 /* GC,UA,G,A,A */ + -30 140 0 140 /* GC,UA,G,A,C */ + -90 80 70 80 /* GC,UA,G,A,G */ + -30 140 0 140 /* GC,UA,G,A,U */ + 10 180 50 180 /* GC,UA,G,C,A */ + 70 180 50 180 /* GC,UA,G,C,C */ + 10 180 50 180 /* GC,UA,G,C,G */ + 70 180 50 180 /* GC,UA,G,C,U */ + -80 90 80 90 /* GC,UA,G,G,A */ + -30 140 0 140 /* GC,UA,G,G,C */ + -10 30 150 30 /* GC,UA,G,G,G */ + -30 140 0 140 /* GC,UA,G,G,U */ + 10 180 50 180 /* GC,UA,G,U,A */ + 40 150 20 150 /* GC,UA,G,U,C */ + 10 180 50 180 /* GC,UA,G,U,G */ + -70 100 90 100 /* GC,UA,G,U,U */ + 190 190 190 170 /* GC,UA,U,A,A */ + 140 140 140 70 /* GC,UA,U,A,C */ + 80 140 80 10 /* GC,UA,U,A,G */ + 140 140 140 70 /* GC,UA,U,A,U */ + 190 190 190 110 /* GC,UA,U,C,A */ + 190 190 190 110 /* GC,UA,U,C,C */ + 190 190 190 110 /* GC,UA,U,C,G */ + 190 190 190 110 /* GC,UA,U,C,U */ + 90 150 90 20 /* GC,UA,U,G,A */ + 140 140 140 70 /* GC,UA,U,G,C */ + 30 30 30 90 /* GC,UA,U,G,G */ + 140 140 140 70 /* GC,UA,U,G,U */ + 190 190 190 110 /* GC,UA,U,U,A */ + 160 160 160 80 /* GC,UA,U,U,C */ + 190 190 190 110 /* GC,UA,U,U,G */ + 100 100 100 30 /* GC,UA,U,U,U */ + 270 230 190 230 /* GU,CG,A,A,A */ + 260 220 180 220 /* GU,CG,A,A,C */ + 170 130 90 130 /* GU,CG,A,A,G */ + 260 220 180 220 /* GU,CG,A,A,U */ + 300 270 230 270 /* GU,CG,A,C,A */ + 290 250 270 250 /* GU,CG,A,C,C */ + 300 270 230 270 /* GU,CG,A,C,G */ + 270 240 260 240 /* GU,CG,A,C,U */ + 170 130 90 130 /* GU,CG,A,G,A */ + 260 220 180 220 /* GU,CG,A,G,C */ + 110 80 170 80 /* GU,CG,A,G,G */ + 260 220 180 220 /* GU,CG,A,G,U */ + 300 270 230 270 /* GU,CG,A,U,A */ + 270 240 260 240 /* GU,CG,A,U,C */ + 300 270 230 270 /* GU,CG,A,U,G */ + 240 150 110 150 /* GU,CG,A,U,U */ + 230 230 230 230 /* GU,CG,C,A,A */ + 220 220 220 220 /* GU,CG,C,A,C */ + 130 190 130 190 /* GU,CG,C,A,G */ + 220 220 220 220 /* GU,CG,C,A,U */ + 270 270 270 270 /* GU,CG,C,C,A */ + 250 250 250 250 /* GU,CG,C,C,C */ + 270 270 270 270 /* GU,CG,C,C,G */ + 240 240 240 240 /* GU,CG,C,C,U */ + 130 190 130 190 /* GU,CG,C,G,A */ + 220 220 220 220 /* GU,CG,C,G,C */ + 80 80 80 80 /* GU,CG,C,G,G */ + 220 220 220 220 /* GU,CG,C,G,U */ + 270 270 270 270 /* GU,CG,C,U,A */ + 240 240 240 240 /* GU,CG,C,U,C */ + 270 270 270 270 /* GU,CG,C,U,G */ + 150 150 150 150 /* GU,CG,C,U,U */ + 150 230 100 230 /* GU,CG,G,A,A */ + 140 220 90 220 /* GU,CG,G,A,C */ + 50 130 130 130 /* GU,CG,G,A,G */ + 140 220 90 220 /* GU,CG,G,A,U */ + 190 270 140 270 /* GU,CG,G,C,A */ + 230 250 120 250 /* GU,CG,G,C,C */ + 190 270 140 270 /* GU,CG,G,C,G */ + 220 240 110 240 /* GU,CG,G,C,U */ + 50 130 130 130 /* GU,CG,G,G,A */ + 140 220 90 220 /* GU,CG,G,G,C */ + 130 80 210 80 /* GU,CG,G,G,G */ + 140 220 90 220 /* GU,CG,G,G,U */ + 190 270 140 270 /* GU,CG,G,U,A */ + 220 240 110 240 /* GU,CG,G,U,C */ + 190 270 140 270 /* GU,CG,G,U,G */ + 70 150 150 150 /* GU,CG,G,U,U */ + 230 230 230 290 /* GU,CG,U,A,A */ + 220 220 220 220 /* GU,CG,U,A,C */ + 130 190 130 130 /* GU,CG,U,A,G */ + 220 220 220 220 /* GU,CG,U,A,U */ + 270 270 270 270 /* GU,CG,U,C,A */ + 250 250 250 250 /* GU,CG,U,C,C */ + 270 270 270 270 /* GU,CG,U,C,G */ + 240 240 240 240 /* GU,CG,U,C,U */ + 130 190 130 130 /* GU,CG,U,G,A */ + 220 220 220 220 /* GU,CG,U,G,C */ + 80 80 80 210 /* GU,CG,U,G,G */ + 220 220 220 220 /* GU,CG,U,G,U */ + 270 270 270 270 /* GU,CG,U,U,A */ + 240 240 240 240 /* GU,CG,U,U,C */ + 270 270 270 270 /* GU,CG,U,U,G */ + 150 150 150 150 /* GU,CG,U,U,U */ + 280 240 200 240 /* GU,GC,A,A,A */ + 250 220 180 220 /* GU,GC,A,A,C */ + 70 40 0 40 /* GU,GC,A,A,G */ + 250 220 180 220 /* GU,GC,A,A,U */ + 250 210 170 210 /* GU,GC,A,C,A */ + 250 220 240 220 /* GU,GC,A,C,C */ + 250 210 170 210 /* GU,GC,A,C,G */ + 250 220 240 220 /* GU,GC,A,C,U */ + 140 100 60 100 /* GU,GC,A,G,A */ + 250 220 180 220 /* GU,GC,A,G,C */ + 110 80 170 80 /* GU,GC,A,G,G */ + 250 220 180 220 /* GU,GC,A,G,U */ + 250 210 170 210 /* GU,GC,A,U,A */ + 260 220 240 220 /* GU,GC,A,U,C */ + 250 210 170 210 /* GU,GC,A,U,G */ + 240 140 100 140 /* GU,GC,A,U,U */ + 240 240 240 240 /* GU,GC,C,A,A */ + 220 220 220 220 /* GU,GC,C,A,C */ + 40 100 40 100 /* GU,GC,C,A,G */ + 220 220 220 220 /* GU,GC,C,A,U */ + 210 210 210 210 /* GU,GC,C,C,A */ + 220 220 220 220 /* GU,GC,C,C,C */ + 210 210 210 210 /* GU,GC,C,C,G */ + 220 220 220 220 /* GU,GC,C,C,U */ + 100 160 100 160 /* GU,GC,C,G,A */ + 220 220 220 220 /* GU,GC,C,G,C */ + 80 80 80 80 /* GU,GC,C,G,G */ + 220 220 220 220 /* GU,GC,C,G,U */ + 210 210 210 210 /* GU,GC,C,U,A */ + 220 220 220 220 /* GU,GC,C,U,C */ + 210 210 210 210 /* GU,GC,C,U,G */ + 140 140 140 140 /* GU,GC,C,U,U */ + 160 240 110 240 /* GU,GC,G,A,A */ + 140 220 90 220 /* GU,GC,G,A,C */ + -40 40 40 40 /* GU,GC,G,A,G */ + 140 220 90 220 /* GU,GC,G,A,U */ + 130 210 80 210 /* GU,GC,G,C,A */ + 200 220 90 220 /* GU,GC,G,C,C */ + 130 210 80 210 /* GU,GC,G,C,G */ + 200 220 90 220 /* GU,GC,G,C,U */ + 20 100 100 100 /* GU,GC,G,G,A */ + 140 220 90 220 /* GU,GC,G,G,C */ + 130 80 210 80 /* GU,GC,G,G,G */ + 140 220 90 220 /* GU,GC,G,G,U */ + 130 210 80 210 /* GU,GC,G,U,A */ + 200 220 90 220 /* GU,GC,G,U,C */ + 130 210 80 210 /* GU,GC,G,U,G */ + 60 140 140 140 /* GU,GC,G,U,U */ + 240 240 240 300 /* GU,GC,U,A,A */ + 220 220 220 220 /* GU,GC,U,A,C */ + 40 100 40 40 /* GU,GC,U,A,G */ + 220 220 220 220 /* GU,GC,U,A,U */ + 210 210 210 210 /* GU,GC,U,C,A */ + 220 220 220 220 /* GU,GC,U,C,C */ + 210 210 210 210 /* GU,GC,U,C,G */ + 220 220 220 220 /* GU,GC,U,C,U */ + 100 160 100 100 /* GU,GC,U,G,A */ + 220 220 220 220 /* GU,GC,U,G,C */ + 80 80 80 210 /* GU,GC,U,G,G */ + 220 220 220 220 /* GU,GC,U,G,U */ + 210 210 210 210 /* GU,GC,U,U,A */ + 220 220 220 220 /* GU,GC,U,U,C */ + 210 210 210 210 /* GU,GC,U,U,G */ + 140 140 140 140 /* GU,GC,U,U,U */ + 410 370 330 370 /* GU,GU,A,A,A */ + 370 340 300 340 /* GU,GU,A,A,C */ + 290 260 220 260 /* GU,GU,A,A,G */ + 370 340 300 340 /* GU,GU,A,A,U */ + 370 340 300 340 /* GU,GU,A,C,A */ + 370 340 360 340 /* GU,GU,A,C,C */ + 370 340 300 340 /* GU,GU,A,C,G */ + 370 340 360 340 /* GU,GU,A,C,U */ + 330 300 260 300 /* GU,GU,A,G,A */ + 370 340 300 340 /* GU,GU,A,G,C */ + 240 210 300 210 /* GU,GU,A,G,G */ + 370 340 300 340 /* GU,GU,A,G,U */ + 370 340 300 340 /* GU,GU,A,U,A */ + 370 340 360 340 /* GU,GU,A,U,C */ + 370 340 300 340 /* GU,GU,A,U,G */ + 430 340 300 340 /* GU,GU,A,U,U */ + 370 370 370 370 /* GU,GU,C,A,A */ + 340 340 340 340 /* GU,GU,C,A,C */ + 260 320 260 320 /* GU,GU,C,A,G */ + 340 340 340 340 /* GU,GU,C,A,U */ + 340 340 340 340 /* GU,GU,C,C,A */ + 340 340 340 340 /* GU,GU,C,C,C */ + 340 340 340 340 /* GU,GU,C,C,G */ + 340 340 340 340 /* GU,GU,C,C,U */ + 300 360 300 360 /* GU,GU,C,G,A */ + 340 340 340 340 /* GU,GU,C,G,C */ + 210 210 210 210 /* GU,GU,C,G,G */ + 340 340 340 340 /* GU,GU,C,G,U */ + 340 340 340 340 /* GU,GU,C,U,A */ + 340 340 340 340 /* GU,GU,C,U,C */ + 340 340 340 340 /* GU,GU,C,U,G */ + 340 340 340 340 /* GU,GU,C,U,U */ + 290 370 240 370 /* GU,GU,G,A,A */ + 260 340 210 340 /* GU,GU,G,A,C */ + 180 260 260 260 /* GU,GU,G,A,G */ + 260 340 210 340 /* GU,GU,G,A,U */ + 260 340 210 340 /* GU,GU,G,C,A */ + 320 340 210 340 /* GU,GU,G,C,C */ + 260 340 210 340 /* GU,GU,G,C,G */ + 320 340 210 340 /* GU,GU,G,C,U */ + 220 300 300 300 /* GU,GU,G,G,A */ + 260 340 210 340 /* GU,GU,G,G,C */ + 260 210 340 210 /* GU,GU,G,G,G */ + 260 340 210 340 /* GU,GU,G,G,U */ + 260 340 210 340 /* GU,GU,G,U,A */ + 320 340 210 340 /* GU,GU,G,U,C */ + 260 340 210 340 /* GU,GU,G,U,G */ + 260 340 340 340 /* GU,GU,G,U,U */ + 370 370 370 430 /* GU,GU,U,A,A */ + 340 340 340 340 /* GU,GU,U,A,C */ + 260 320 260 260 /* GU,GU,U,A,G */ + 340 340 340 340 /* GU,GU,U,A,U */ + 340 340 340 340 /* GU,GU,U,C,A */ + 340 340 340 340 /* GU,GU,U,C,C */ + 340 340 340 340 /* GU,GU,U,C,G */ + 340 340 340 340 /* GU,GU,U,C,U */ + 300 360 300 300 /* GU,GU,U,G,A */ + 340 340 340 340 /* GU,GU,U,G,C */ + 210 210 210 340 /* GU,GU,U,G,G */ + 340 340 340 340 /* GU,GU,U,G,U */ + 340 340 340 340 /* GU,GU,U,U,A */ + 340 340 340 340 /* GU,GU,U,U,C */ + 340 340 340 340 /* GU,GU,U,U,G */ + 340 340 340 340 /* GU,GU,U,U,U */ + 360 270 360 270 /* GU,UG,A,A,A */ + 340 310 270 310 /* GU,UG,A,A,C */ + 220 170 130 170 /* GU,UG,A,A,G */ + 340 310 270 310 /* GU,UG,A,A,U */ + 340 310 270 310 /* GU,UG,A,C,A */ + 340 310 330 310 /* GU,UG,A,C,C */ + 340 310 270 310 /* GU,UG,A,C,G */ + 340 310 330 310 /* GU,UG,A,C,U */ + 370 340 300 340 /* GU,UG,A,G,A */ + 340 310 270 310 /* GU,UG,A,G,C */ + 210 180 270 180 /* GU,UG,A,G,G */ + 340 310 270 310 /* GU,UG,A,G,U */ + 340 310 270 310 /* GU,UG,A,U,A */ + 340 310 330 310 /* GU,UG,A,U,C */ + 340 310 270 310 /* GU,UG,A,U,G */ + 400 310 270 310 /* GU,UG,A,U,U */ + 270 270 270 270 /* GU,UG,C,A,A */ + 310 310 310 310 /* GU,UG,C,A,C */ + 170 230 170 230 /* GU,UG,C,A,G */ + 310 310 310 310 /* GU,UG,C,A,U */ + 310 310 310 310 /* GU,UG,C,C,A */ + 310 310 310 310 /* GU,UG,C,C,C */ + 310 310 310 310 /* GU,UG,C,C,G */ + 310 310 310 310 /* GU,UG,C,C,U */ + 340 400 340 400 /* GU,UG,C,G,A */ + 310 310 310 310 /* GU,UG,C,G,C */ + 180 180 180 180 /* GU,UG,C,G,G */ + 310 310 310 310 /* GU,UG,C,G,U */ + 310 310 310 310 /* GU,UG,C,U,A */ + 310 310 310 310 /* GU,UG,C,U,C */ + 310 310 310 310 /* GU,UG,C,U,G */ + 310 310 310 310 /* GU,UG,C,U,U */ + 190 270 140 270 /* GU,UG,G,A,A */ + 230 310 180 310 /* GU,UG,G,A,C */ + 20 170 170 170 /* GU,UG,G,A,G */ + 230 310 180 310 /* GU,UG,G,A,U */ + 230 310 180 310 /* GU,UG,G,C,A */ + 290 310 180 310 /* GU,UG,G,C,C */ + 230 310 180 310 /* GU,UG,G,C,G */ + 290 310 180 310 /* GU,UG,G,C,U */ + 260 340 340 340 /* GU,UG,G,G,A */ + 230 310 180 310 /* GU,UG,G,G,C */ + 230 180 310 180 /* GU,UG,G,G,G */ + 230 310 180 310 /* GU,UG,G,G,U */ + 230 310 180 310 /* GU,UG,G,U,A */ + 290 310 180 310 /* GU,UG,G,U,C */ + 230 310 180 310 /* GU,UG,G,U,G */ + 230 310 310 310 /* GU,UG,G,U,U */ + 270 270 270 330 /* GU,UG,U,A,A */ + 310 310 310 310 /* GU,UG,U,A,C */ + 170 230 170 170 /* GU,UG,U,A,G */ + 310 310 310 310 /* GU,UG,U,A,U */ + 310 310 310 310 /* GU,UG,U,C,A */ + 310 310 310 310 /* GU,UG,U,C,C */ + 310 310 310 310 /* GU,UG,U,C,G */ + 310 310 310 310 /* GU,UG,U,C,U */ + 340 400 340 340 /* GU,UG,U,G,A */ + 310 310 310 310 /* GU,UG,U,G,C */ + 180 180 180 310 /* GU,UG,U,G,G */ + 310 310 310 310 /* GU,UG,U,G,U */ + 310 310 310 310 /* GU,UG,U,U,A */ + 310 310 310 310 /* GU,UG,U,U,C */ + 310 310 310 310 /* GU,UG,U,U,G */ + 310 310 310 310 /* GU,UG,U,U,U */ + 340 310 270 310 /* GU,AU,A,A,A */ + 320 280 240 280 /* GU,AU,A,A,C */ + 220 180 140 180 /* GU,AU,A,A,G */ + 320 280 240 280 /* GU,AU,A,A,U */ + 330 290 250 290 /* GU,AU,A,C,A */ + 320 290 310 290 /* GU,AU,A,C,C */ + 330 290 250 290 /* GU,AU,A,C,G */ + 320 290 310 290 /* GU,AU,A,C,U */ + 290 250 210 250 /* GU,AU,A,G,A */ + 320 280 240 280 /* GU,AU,A,G,C */ + 170 130 220 130 /* GU,AU,A,G,G */ + 320 280 240 280 /* GU,AU,A,G,U */ + 330 290 250 290 /* GU,AU,A,U,A */ + 320 290 310 290 /* GU,AU,A,U,C */ + 330 290 250 290 /* GU,AU,A,U,G */ + 290 200 160 200 /* GU,AU,A,U,U */ + 310 310 310 310 /* GU,AU,C,A,A */ + 280 280 280 280 /* GU,AU,C,A,C */ + 180 240 180 240 /* GU,AU,C,A,G */ + 280 280 280 280 /* GU,AU,C,A,U */ + 290 290 290 290 /* GU,AU,C,C,A */ + 290 290 290 290 /* GU,AU,C,C,C */ + 290 290 290 290 /* GU,AU,C,C,G */ + 290 290 290 290 /* GU,AU,C,C,U */ + 250 310 250 310 /* GU,AU,C,G,A */ + 280 280 280 280 /* GU,AU,C,G,C */ + 130 130 130 130 /* GU,AU,C,G,G */ + 280 280 280 280 /* GU,AU,C,G,U */ + 290 290 290 290 /* GU,AU,C,U,A */ + 290 290 290 290 /* GU,AU,C,U,C */ + 290 290 290 290 /* GU,AU,C,U,G */ + 200 200 200 200 /* GU,AU,C,U,U */ + 230 310 180 310 /* GU,AU,G,A,A */ + 200 280 150 280 /* GU,AU,G,A,C */ + 100 180 180 180 /* GU,AU,G,A,G */ + 200 280 150 280 /* GU,AU,G,A,U */ + 210 290 160 290 /* GU,AU,G,C,A */ + 270 290 160 290 /* GU,AU,G,C,C */ + 210 290 160 290 /* GU,AU,G,C,G */ + 270 290 160 290 /* GU,AU,G,C,U */ + 170 250 250 250 /* GU,AU,G,G,A */ + 200 280 150 280 /* GU,AU,G,G,C */ + 180 130 260 130 /* GU,AU,G,G,G */ + 200 280 150 280 /* GU,AU,G,G,U */ + 210 290 160 290 /* GU,AU,G,U,A */ + 270 290 160 290 /* GU,AU,G,U,C */ + 210 290 160 290 /* GU,AU,G,U,G */ + 120 200 200 200 /* GU,AU,G,U,U */ + 310 310 310 370 /* GU,AU,U,A,A */ + 280 280 280 280 /* GU,AU,U,A,C */ + 180 240 180 180 /* GU,AU,U,A,G */ + 280 280 280 280 /* GU,AU,U,A,U */ + 290 290 290 290 /* GU,AU,U,C,A */ + 290 290 290 290 /* GU,AU,U,C,C */ + 290 290 290 290 /* GU,AU,U,C,G */ + 290 290 290 290 /* GU,AU,U,C,U 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120 /* UG,UA,C,G,G */ + 230 230 230 230 /* UG,UA,C,G,U */ + 280 280 280 280 /* UG,UA,C,U,A */ + 250 250 250 250 /* UG,UA,C,U,C */ + 280 280 280 280 /* UG,UA,C,U,G */ + 190 190 190 190 /* UG,UA,C,U,U */ + 140 280 150 280 /* UG,UA,G,A,A */ + 100 230 100 230 /* UG,UA,G,A,C */ + 40 170 170 170 /* UG,UA,G,A,G */ + 100 230 100 230 /* UG,UA,G,A,U */ + 140 280 150 280 /* UG,UA,G,C,A */ + 200 280 150 280 /* UG,UA,G,C,C */ + 140 280 150 280 /* UG,UA,G,C,G */ + 200 280 150 280 /* UG,UA,G,C,U */ + 50 180 180 180 /* UG,UA,G,G,A */ + 100 230 100 230 /* UG,UA,G,G,C */ + 120 120 250 120 /* UG,UA,G,G,G */ + 100 230 100 230 /* UG,UA,G,G,U */ + 140 280 150 280 /* UG,UA,G,U,A */ + 170 250 120 250 /* UG,UA,G,U,C */ + 140 280 150 280 /* UG,UA,G,U,G */ + 60 190 190 190 /* UG,UA,G,U,U */ + 280 280 280 340 /* UG,UA,U,A,A */ + 230 230 230 230 /* UG,UA,U,A,C */ + 170 230 170 170 /* UG,UA,U,A,G */ + 230 230 230 230 /* UG,UA,U,A,U */ + 280 280 280 280 /* UG,UA,U,C,A */ + 280 280 280 280 /* UG,UA,U,C,C */ + 280 280 280 280 /* UG,UA,U,C,G */ + 280 280 280 280 /* UG,UA,U,C,U */ + 180 240 180 180 /* UG,UA,U,G,A */ + 230 230 230 230 /* UG,UA,U,G,C */ + 120 120 120 250 /* UG,UA,U,G,G */ + 230 230 230 230 /* UG,UA,U,G,U */ + 280 280 280 280 /* UG,UA,U,U,A */ + 250 250 250 250 /* UG,UA,U,U,C */ + 280 280 280 280 /* UG,UA,U,U,G */ + 190 190 190 190 /* UG,UA,U,U,U */ + 200 180 140 180 /* AU,CG,A,A,A */ + 190 180 140 180 /* AU,CG,A,A,C */ + 100 90 50 90 /* AU,CG,A,A,G */ + 190 180 140 180 /* AU,CG,A,A,U */ + 240 220 180 220 /* AU,CG,A,C,A */ + 220 210 230 210 /* AU,CG,A,C,C */ + 240 220 180 220 /* AU,CG,A,C,G */ + 210 190 210 190 /* AU,CG,A,C,U */ + 100 90 50 90 /* AU,CG,A,G,A */ + 190 180 140 180 /* AU,CG,A,G,C */ + 50 30 120 30 /* AU,CG,A,G,G */ + 190 180 140 180 /* AU,CG,A,G,U */ + 240 220 180 220 /* AU,CG,A,U,A */ + 210 190 210 190 /* AU,CG,A,U,C */ + 240 220 180 220 /* AU,CG,A,U,G */ + 180 100 60 100 /* AU,CG,A,U,U */ + 170 180 170 180 /* AU,CG,C,A,A */ + 170 170 170 170 /* AU,CG,C,A,C */ + 80 140 80 140 /* AU,CG,C,A,G */ + 170 170 170 170 /* AU,CG,C,A,U */ + 210 220 210 220 /* AU,CG,C,C,A */ + 200 200 200 200 /* AU,CG,C,C,C */ + 210 220 210 220 /* AU,CG,C,C,G */ + 180 190 180 190 /* AU,CG,C,C,U */ + 80 140 80 140 /* AU,CG,C,G,A */ + 170 170 170 170 /* AU,CG,C,G,C */ + 20 30 20 30 /* AU,CG,C,G,G */ + 170 170 170 170 /* AU,CG,C,G,U */ + 210 220 210 220 /* AU,CG,C,U,A */ + 180 190 180 190 /* AU,CG,C,U,C */ + 210 220 210 220 /* AU,CG,C,U,G */ + 90 100 90 100 /* AU,CG,C,U,U */ + 70 180 20 180 /* AU,CG,G,A,A */ + 70 180 20 180 /* AU,CG,G,A,C */ + -20 90 60 90 /* AU,CG,G,A,G */ + 70 180 20 180 /* AU,CG,G,A,U */ + 110 220 60 220 /* AU,CG,G,C,A */ + 160 210 50 210 /* AU,CG,G,C,C */ + 110 220 60 220 /* AU,CG,G,C,G */ + 140 190 30 190 /* AU,CG,G,C,U */ + -20 90 60 90 /* AU,CG,G,G,A */ + 70 180 20 180 /* AU,CG,G,G,C */ + 50 30 130 30 /* AU,CG,G,G,G */ + 70 180 20 180 /* AU,CG,G,G,U */ + 110 220 60 220 /* AU,CG,G,U,A */ + 140 190 30 190 /* AU,CG,G,U,C */ + 110 220 60 220 /* AU,CG,G,U,G */ + 0 100 70 100 /* AU,CG,G,U,U */ + 170 180 170 150 /* AU,CG,U,A,A */ + 170 170 170 80 /* AU,CG,U,A,C */ + 80 140 80 0 /* AU,CG,U,A,G */ + 170 170 170 80 /* AU,CG,U,A,U */ + 210 220 210 130 /* AU,CG,U,C,A */ + 200 200 200 110 /* AU,CG,U,C,C */ + 210 220 210 130 /* AU,CG,U,C,G */ + 180 190 180 100 /* AU,CG,U,C,U */ + 80 140 80 0 /* AU,CG,U,G,A */ + 170 170 170 80 /* AU,CG,U,G,C */ + 20 30 20 70 /* AU,CG,U,G,G */ + 170 170 170 80 /* AU,CG,U,G,U */ + 210 220 210 130 /* AU,CG,U,U,A */ + 180 190 180 100 /* AU,CG,U,U,C */ + 210 220 210 130 /* AU,CG,U,U,G */ + 90 100 90 10 /* AU,CG,U,U,U */ + 210 200 160 200 /* AU,GC,A,A,A */ + 190 170 130 170 /* AU,GC,A,A,C */ + 10 0 -40 0 /* AU,GC,A,A,G */ + 190 170 130 170 /* AU,GC,A,A,U */ + 180 170 130 170 /* AU,GC,A,C,A */ + 190 170 190 170 /* AU,GC,A,C,C */ + 180 170 130 170 /* AU,GC,A,C,G */ + 190 170 190 170 /* AU,GC,A,C,U */ + 70 60 20 60 /* AU,GC,A,G,A */ + 190 170 130 170 /* AU,GC,A,G,C */ + 50 30 120 30 /* AU,GC,A,G,G */ + 190 170 130 170 /* AU,GC,A,G,U */ + 180 170 130 170 /* AU,GC,A,U,A */ + 190 180 200 180 /* AU,GC,A,U,C */ + 180 170 130 170 /* AU,GC,A,U,G */ + 170 100 60 100 /* AU,GC,A,U,U */ + 190 190 190 190 /* AU,GC,C,A,A */ + 160 170 160 170 /* AU,GC,C,A,C */ + -10 50 -10 50 /* AU,GC,C,A,G */ + 160 170 160 170 /* AU,GC,C,A,U */ + 160 160 160 160 /* AU,GC,C,C,A */ + 160 170 160 170 /* AU,GC,C,C,C */ + 160 160 160 160 /* AU,GC,C,C,G */ + 160 170 160 170 /* AU,GC,C,C,U */ + 50 110 50 110 /* AU,GC,C,G,A */ + 160 170 160 170 /* AU,GC,C,G,C */ + 20 30 20 30 /* AU,GC,C,G,G */ + 160 170 160 170 /* AU,GC,C,G,U */ + 160 160 160 160 /* AU,GC,C,U,A */ + 170 170 170 170 /* AU,GC,C,U,C */ + 160 160 160 160 /* AU,GC,C,U,G */ + 90 90 90 90 /* AU,GC,C,U,U */ + 90 200 40 200 /* AU,GC,G,A,A */ + 60 170 10 170 /* AU,GC,G,A,C */ + -110 0 -30 0 /* AU,GC,G,A,G */ + 60 170 10 170 /* AU,GC,G,A,U */ + 60 170 10 170 /* AU,GC,G,C,A */ + 120 170 10 170 /* AU,GC,G,C,C */ + 60 170 10 170 /* AU,GC,G,C,G */ + 120 170 10 170 /* AU,GC,G,C,U */ + -50 60 30 60 /* AU,GC,G,G,A */ + 60 170 10 170 /* AU,GC,G,G,C */ + 50 30 130 30 /* AU,GC,G,G,G */ + 60 170 10 170 /* AU,GC,G,G,U */ + 60 170 10 170 /* AU,GC,G,U,A */ + 130 180 20 180 /* AU,GC,G,U,C */ + 60 170 10 170 /* AU,GC,G,U,G */ + -10 100 70 100 /* AU,GC,G,U,U */ + 190 190 190 160 /* AU,GC,U,A,A */ + 160 170 160 80 /* AU,GC,U,A,C */ + -10 50 -10 -100 /* AU,GC,U,A,G */ + 160 170 160 80 /* AU,GC,U,A,U */ + 160 160 160 70 /* AU,GC,U,C,A */ + 160 170 160 80 /* AU,GC,U,C,C */ + 160 160 160 70 /* AU,GC,U,C,G */ + 160 170 160 80 /* AU,GC,U,C,U */ + 50 110 50 -30 /* AU,GC,U,G,A */ + 160 170 160 80 /* AU,GC,U,G,C */ + 20 30 20 70 /* AU,GC,U,G,G */ + 160 170 160 80 /* AU,GC,U,G,U */ + 160 160 160 70 /* AU,GC,U,U,A */ + 170 170 170 80 /* AU,GC,U,U,C */ + 160 160 160 70 /* AU,GC,U,U,G */ + 90 90 90 0 /* AU,GC,U,U,U */ + 340 330 290 330 /* AU,GU,A,A,A */ + 310 290 250 290 /* AU,GU,A,A,C */ + 230 210 170 210 /* AU,GU,A,A,G */ + 310 290 250 290 /* AU,GU,A,A,U */ + 310 290 250 290 /* AU,GU,A,C,A */ 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AU,GU,G,A,A */ + 180 290 130 290 /* AU,GU,G,A,C */ + 100 210 180 210 /* AU,GU,G,A,G */ + 180 290 130 290 /* AU,GU,G,A,U */ + 180 290 130 290 /* AU,GU,G,C,A */ + 240 290 130 290 /* AU,GU,G,C,C */ + 180 290 130 290 /* AU,GU,G,C,G */ + 240 290 130 290 /* AU,GU,G,C,U */ + 140 250 220 250 /* AU,GU,G,G,A */ + 180 290 130 290 /* AU,GU,G,G,C */ + 180 160 260 160 /* AU,GU,G,G,G */ + 180 290 130 290 /* AU,GU,G,G,U */ + 180 290 130 290 /* AU,GU,G,U,A */ + 240 290 130 290 /* AU,GU,G,U,C */ + 180 290 130 290 /* AU,GU,G,U,G */ + 180 290 260 290 /* AU,GU,G,U,U */ + 320 320 320 290 /* AU,GU,U,A,A */ + 280 290 280 200 /* AU,GU,U,A,C */ + 200 270 200 120 /* AU,GU,U,A,G */ + 280 290 280 200 /* AU,GU,U,A,U */ + 280 290 280 200 /* AU,GU,U,C,A */ + 280 290 280 200 /* AU,GU,U,C,C */ + 280 290 280 200 /* AU,GU,U,C,G */ + 280 290 280 200 /* AU,GU,U,C,U */ + 240 310 240 160 /* AU,GU,U,G,A */ + 280 290 280 200 /* AU,GU,U,G,C */ + 150 160 150 200 /* AU,GU,U,G,G */ + 280 290 280 200 /* AU,GU,U,G,U */ + 280 290 280 200 /* AU,GU,U,U,A */ + 280 290 280 200 /* AU,GU,U,U,C */ + 280 290 280 200 /* AU,GU,U,U,G */ + 280 290 280 200 /* AU,GU,U,U,U */ + 240 230 190 230 /* AU,UG,A,A,A */ + 280 260 220 260 /* AU,UG,A,A,C */ + 140 130 90 130 /* AU,UG,A,A,G */ + 280 260 220 260 /* AU,UG,A,A,U */ + 280 260 220 260 /* AU,UG,A,C,A */ + 280 260 280 260 /* AU,UG,A,C,C */ + 280 260 220 260 /* AU,UG,A,C,G */ + 280 260 280 260 /* AU,UG,A,C,U */ + 310 290 250 290 /* AU,UG,A,G,A */ + 280 260 220 260 /* AU,UG,A,G,C */ + 150 130 220 130 /* AU,UG,A,G,G */ + 280 260 220 260 /* AU,UG,A,G,U */ + 280 260 220 260 /* AU,UG,A,U,A */ + 280 260 280 260 /* AU,UG,A,U,C */ + 280 260 220 260 /* AU,UG,A,U,G */ + 340 260 220 260 /* AU,UG,A,U,U */ + 220 220 220 220 /* AU,UG,C,A,A */ + 250 260 250 260 /* AU,UG,C,A,C */ + 120 180 120 180 /* AU,UG,C,A,G */ + 250 260 250 260 /* AU,UG,C,A,U */ + 250 260 250 260 /* AU,UG,C,C,A */ + 250 260 250 260 /* AU,UG,C,C,C */ + 250 260 250 260 /* AU,UG,C,C,G */ + 250 260 250 260 /* AU,UG,C,C,U */ + 280 350 280 350 /* AU,UG,C,G,A */ + 250 260 250 260 /* AU,UG,C,G,C */ + 120 130 120 130 /* AU,UG,C,G,G */ + 250 260 250 260 /* AU,UG,C,G,U */ + 250 260 250 260 /* AU,UG,C,U,A */ + 250 260 250 260 /* AU,UG,C,U,C */ + 250 260 250 260 /* AU,UG,C,U,G */ + 250 260 250 260 /* AU,UG,C,U,U */ + 120 230 70 230 /* AU,UG,G,A,A */ + 150 260 100 260 /* AU,UG,G,A,C */ + 20 130 100 130 /* AU,UG,G,A,G */ + 150 260 100 260 /* AU,UG,G,A,U */ + 150 260 100 260 /* AU,UG,G,C,A */ + 210 260 100 260 /* AU,UG,G,C,C */ + 150 260 100 260 /* AU,UG,G,C,G */ + 210 260 100 260 /* AU,UG,G,C,U */ + 180 290 260 290 /* AU,UG,G,G,A */ + 150 260 100 260 /* AU,UG,G,G,C */ + 150 130 230 130 /* AU,UG,G,G,G */ + 150 260 100 260 /* AU,UG,G,G,U */ + 150 260 100 260 /* AU,UG,G,U,A */ + 210 260 100 260 /* AU,UG,G,U,C */ + 150 260 100 260 /* AU,UG,G,U,G */ + 150 260 230 260 /* AU,UG,G,U,U */ + 220 220 220 190 /* AU,UG,U,A,A */ + 250 260 250 170 /* AU,UG,U,A,C */ + 120 180 120 30 /* AU,UG,U,A,G */ + 250 260 250 170 /* AU,UG,U,A,U */ + 250 260 250 170 /* AU,UG,U,C,A */ + 250 260 250 170 /* AU,UG,U,C,C */ + 250 260 250 170 /* AU,UG,U,C,G */ + 250 260 250 170 /* AU,UG,U,C,U */ + 280 350 280 200 /* AU,UG,U,G,A */ + 250 260 250 170 /* AU,UG,U,G,C */ + 120 130 120 170 /* AU,UG,U,G,G */ + 250 260 250 170 /* AU,UG,U,G,U */ + 250 260 250 170 /* AU,UG,U,U,A */ + 250 260 250 170 /* AU,UG,U,U,C */ + 250 260 250 170 /* AU,UG,U,U,G */ + 250 260 250 170 /* AU,UG,U,U,U */ + 280 260 220 260 /* AU,AU,A,A,A */ + 250 240 200 240 /* AU,AU,A,A,C */ + 150 140 100 140 /* AU,AU,A,A,G */ + 250 240 200 240 /* AU,AU,A,A,U */ + 260 250 210 250 /* AU,AU,A,C,A */ + 260 240 260 240 /* AU,AU,A,C,C */ + 260 250 210 250 /* AU,AU,A,C,G */ + 260 240 260 240 /* AU,AU,A,C,U */ + 220 210 170 210 /* AU,AU,A,G,A */ + 250 240 200 240 /* AU,AU,A,G,C */ + 100 90 180 90 /* AU,AU,A,G,G */ + 250 240 200 240 /* AU,AU,A,G,U */ + 260 250 210 250 /* AU,AU,A,U,A */ + 260 240 260 240 /* AU,AU,A,U,C */ + 260 250 210 250 /* AU,AU,A,U,G */ + 230 150 110 150 /* AU,AU,A,U,U 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140 250 90 250 /* AU,AU,G,U,A */ + 190 240 80 240 /* AU,AU,G,U,C */ + 140 250 90 250 /* AU,AU,G,U,G */ + 40 150 120 150 /* AU,AU,G,U,U */ + 250 260 250 230 /* AU,AU,U,A,A */ + 230 230 230 140 /* AU,AU,U,A,C */ + 130 190 130 40 /* AU,AU,U,A,G */ + 230 230 230 140 /* AU,AU,U,A,U */ + 240 240 240 150 /* AU,AU,U,C,A */ + 230 240 230 150 /* AU,AU,U,C,C */ + 240 240 240 150 /* AU,AU,U,C,G */ + 230 240 230 150 /* AU,AU,U,C,U */ + 200 260 200 110 /* AU,AU,U,G,A */ + 230 230 230 140 /* AU,AU,U,G,C */ + 80 80 80 120 /* AU,AU,U,G,G */ + 230 230 230 140 /* AU,AU,U,G,U */ + 240 240 240 150 /* AU,AU,U,U,A */ + 230 240 230 150 /* AU,AU,U,U,C */ + 240 240 240 150 /* AU,AU,U,U,G */ + 140 150 140 60 /* AU,AU,U,U,U */ + 280 260 220 260 /* AU,UA,A,A,A */ + 230 220 180 220 /* AU,UA,A,A,C */ + 170 160 120 160 /* AU,UA,A,A,G */ + 230 220 180 220 /* AU,UA,A,A,U */ + 280 260 220 260 /* AU,UA,A,C,A */ + 280 260 280 260 /* AU,UA,A,C,C */ + 280 260 220 260 /* AU,UA,A,C,G */ + 280 260 280 260 /* AU,UA,A,C,U */ + 180 170 130 170 /* AU,UA,A,G,A */ + 230 220 180 220 /* AU,UA,A,G,C */ + 120 110 200 110 /* AU,UA,A,G,G */ + 230 220 180 220 /* AU,UA,A,G,U */ + 280 260 220 260 /* AU,UA,A,U,A */ + 250 230 250 230 /* AU,UA,A,U,C */ + 280 260 220 260 /* AU,UA,A,U,G */ + 250 180 140 180 /* AU,UA,A,U,U */ + 250 260 250 260 /* AU,UA,C,A,A */ + 210 210 210 210 /* AU,UA,C,A,C */ + 150 210 150 210 /* AU,UA,C,A,G */ + 210 210 210 210 /* AU,UA,C,A,U */ + 250 260 250 260 /* AU,UA,C,C,A */ + 250 260 250 260 /* AU,UA,C,C,C */ + 250 260 250 260 /* AU,UA,C,C,G */ + 250 260 250 260 /* AU,UA,C,C,U */ + 160 220 160 220 /* AU,UA,C,G,A */ + 210 210 210 210 /* AU,UA,C,G,C */ + 100 100 100 100 /* AU,UA,C,G,G */ + 210 210 210 210 /* AU,UA,C,G,U */ + 250 260 250 260 /* AU,UA,C,U,A */ + 220 230 220 230 /* AU,UA,C,U,C */ + 250 260 250 260 /* AU,UA,C,U,G */ + 170 170 170 170 /* AU,UA,C,U,U */ + 150 260 100 260 /* AU,UA,G,A,A */ + 110 220 60 220 /* AU,UA,G,A,C */ + 50 160 130 160 /* AU,UA,G,A,G */ + 110 220 60 220 /* AU,UA,G,A,U 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*/ + 200 200 100 200 /* UA,CG,A,A,A */ + 190 190 100 190 /* UA,CG,A,A,C */ + 100 100 10 100 /* UA,CG,A,A,G */ + 190 190 100 190 /* UA,CG,A,A,U */ + 240 240 140 240 /* UA,CG,A,C,A */ + 220 220 190 220 /* UA,CG,A,C,C */ + 240 240 140 240 /* UA,CG,A,C,G */ + 210 210 170 210 /* UA,CG,A,C,U */ + 100 100 10 100 /* UA,CG,A,G,A */ + 190 190 100 190 /* UA,CG,A,G,C */ + 50 50 80 50 /* UA,CG,A,G,G */ + 190 190 100 190 /* UA,CG,A,G,U */ + 240 240 140 240 /* UA,CG,A,U,A */ + 210 210 170 210 /* UA,CG,A,U,C */ + 240 240 140 240 /* UA,CG,A,U,G */ + 180 120 20 120 /* UA,CG,A,U,U */ + 150 200 150 170 /* UA,CG,C,A,A */ + 150 190 150 160 /* UA,CG,C,A,C */ + 60 160 60 130 /* UA,CG,C,A,G */ + 150 190 150 160 /* UA,CG,C,A,U */ + 190 240 190 210 /* UA,CG,C,C,A */ + 180 220 180 190 /* UA,CG,C,C,C */ + 190 240 190 210 /* UA,CG,C,C,G */ + 160 210 160 180 /* UA,CG,C,C,U */ + 60 160 60 130 /* UA,CG,C,G,A */ + 150 190 150 160 /* UA,CG,C,G,C */ + 0 50 0 20 /* UA,CG,C,G,G */ + 150 190 150 160 /* UA,CG,C,G,U */ + 190 240 190 210 /* UA,CG,C,U,A */ + 160 210 160 180 /* UA,CG,C,U,C */ + 190 240 190 210 /* UA,CG,C,U,G */ + 70 120 70 90 /* UA,CG,C,U,U */ + 90 200 40 200 /* UA,CG,G,A,A */ + 90 190 40 190 /* UA,CG,G,A,C */ + 0 100 80 100 /* UA,CG,G,A,G */ + 90 190 40 190 /* UA,CG,G,A,U */ + 130 240 80 240 /* UA,CG,G,C,A */ + 180 220 70 220 /* UA,CG,G,C,C */ + 130 240 80 240 /* UA,CG,G,C,G */ + 160 210 50 210 /* UA,CG,G,C,U */ + 0 100 80 100 /* UA,CG,G,G,A */ + 90 190 40 190 /* UA,CG,G,G,C */ + 70 50 150 50 /* UA,CG,G,G,G */ + 90 190 40 190 /* UA,CG,G,G,U */ + 130 240 80 240 /* UA,CG,G,U,A */ + 160 210 50 210 /* UA,CG,G,U,C */ + 130 240 80 240 /* UA,CG,G,U,G */ + 10 120 90 120 /* UA,CG,G,U,U */ + 150 200 150 170 /* UA,CG,U,A,A */ + 150 190 150 110 /* UA,CG,U,A,C */ + 60 160 60 20 /* UA,CG,U,A,G */ + 150 190 150 110 /* UA,CG,U,A,U */ + 190 240 190 150 /* UA,CG,U,C,A */ + 180 220 180 140 /* UA,CG,U,C,C */ + 190 240 190 150 /* UA,CG,U,C,G */ + 160 210 160 120 /* UA,CG,U,C,U */ + 60 160 60 20 /* UA,CG,U,G,A */ + 150 190 150 110 /* UA,CG,U,G,C */ + 0 50 0 90 /* UA,CG,U,G,G */ + 150 190 150 110 /* UA,CG,U,G,U */ + 190 240 190 150 /* UA,CG,U,U,A */ + 160 210 160 120 /* UA,CG,U,U,C */ + 190 240 190 150 /* UA,CG,U,U,G */ + 70 120 70 30 /* UA,CG,U,U,U */ + 210 210 120 210 /* UA,GC,A,A,A */ + 190 190 90 190 /* UA,GC,A,A,C */ + 10 10 -80 10 /* UA,GC,A,A,G */ + 190 190 90 190 /* UA,GC,A,A,U */ + 180 180 90 180 /* UA,GC,A,C,A */ + 190 190 150 190 /* UA,GC,A,C,C */ + 180 180 90 180 /* UA,GC,A,C,G */ + 190 190 150 190 /* UA,GC,A,C,U */ + 70 70 -20 70 /* UA,GC,A,G,A */ + 190 190 90 190 /* UA,GC,A,G,C */ + 50 50 80 50 /* UA,GC,A,G,G */ + 190 190 90 190 /* UA,GC,A,G,U */ + 180 180 90 180 /* UA,GC,A,U,A */ + 190 190 160 190 /* UA,GC,A,U,C */ + 180 180 90 180 /* UA,GC,A,U,G */ + 170 110 20 110 /* UA,GC,A,U,U */ + 170 210 170 180 /* UA,GC,C,A,A */ + 140 190 140 160 /* UA,GC,C,A,C */ + -30 70 -30 40 /* UA,GC,C,A,G */ + 140 190 140 160 /* UA,GC,C,A,U */ + 140 180 140 150 /* UA,GC,C,C,A */ + 140 190 140 160 /* UA,GC,C,C,C */ + 140 180 140 150 /* UA,GC,C,C,G */ + 140 190 140 160 /* UA,GC,C,C,U */ + 30 130 30 100 /* UA,GC,C,G,A */ + 140 190 140 160 /* UA,GC,C,G,C */ + 0 50 0 20 /* UA,GC,C,G,G */ + 140 190 140 160 /* UA,GC,C,G,U */ + 140 180 140 150 /* UA,GC,C,U,A */ + 150 190 150 160 /* UA,GC,C,U,C */ + 140 180 140 150 /* UA,GC,C,U,G */ + 70 110 70 80 /* UA,GC,C,U,U */ + 110 210 60 210 /* UA,GC,G,A,A */ + 80 190 30 190 /* UA,GC,G,A,C */ + -90 10 -10 10 /* UA,GC,G,A,G */ + 80 190 30 190 /* UA,GC,G,A,U */ + 80 180 30 180 /* UA,GC,G,C,A */ + 140 190 30 190 /* UA,GC,G,C,C */ + 80 180 30 180 /* UA,GC,G,C,G */ + 140 190 30 190 /* UA,GC,G,C,U */ + -30 70 50 70 /* UA,GC,G,G,A */ + 80 190 30 190 /* UA,GC,G,G,C */ + 70 50 150 50 /* UA,GC,G,G,G */ + 80 190 30 190 /* UA,GC,G,G,U */ + 80 180 30 180 /* UA,GC,G,U,A */ + 150 190 40 190 /* UA,GC,G,U,C */ + 80 180 30 180 /* UA,GC,G,U,G */ + 10 110 90 110 /* UA,GC,G,U,U */ + 170 210 170 190 /* UA,GC,U,A,A */ + 140 190 140 100 /* UA,GC,U,A,C */ + -30 70 -30 -70 /* UA,GC,U,A,G */ + 140 190 140 100 /* UA,GC,U,A,U */ + 140 180 140 100 /* UA,GC,U,C,A */ + 140 190 140 100 /* UA,GC,U,C,C */ + 140 180 140 100 /* UA,GC,U,C,G */ + 140 190 140 100 /* UA,GC,U,C,U */ + 30 130 30 -10 /* UA,GC,U,G,A */ + 140 190 140 100 /* UA,GC,U,G,C */ + 0 50 0 90 /* UA,GC,U,G,G */ + 140 190 140 100 /* UA,GC,U,G,U */ + 140 180 140 100 /* UA,GC,U,U,A */ + 150 190 150 110 /* UA,GC,U,U,C */ + 140 180 140 100 /* UA,GC,U,U,G */ + 70 110 70 30 /* UA,GC,U,U,U */ + 340 340 250 340 /* UA,GU,A,A,A */ + 310 310 210 310 /* UA,GU,A,A,C */ + 230 230 130 230 /* UA,GU,A,A,G */ + 310 310 210 310 /* UA,GU,A,A,U */ + 310 310 210 310 /* UA,GU,A,C,A */ + 310 310 270 310 /* UA,GU,A,C,C */ + 310 310 210 310 /* UA,GU,A,C,G */ + 310 310 270 310 /* UA,GU,A,C,U */ + 270 270 170 270 /* UA,GU,A,G,A */ + 310 310 210 310 /* UA,GU,A,G,C */ + 180 180 210 180 /* UA,GU,A,G,G */ + 310 310 210 310 /* UA,GU,A,G,U */ + 310 310 210 310 /* UA,GU,A,U,A */ + 310 310 270 310 /* UA,GU,A,U,C */ + 310 310 210 310 /* UA,GU,A,U,G */ + 370 310 210 310 /* UA,GU,A,U,U */ + 300 340 300 310 /* UA,GU,C,A,A */ + 260 310 260 280 /* UA,GU,C,A,C */ + 180 290 180 260 /* UA,GU,C,A,G */ + 260 310 260 280 /* UA,GU,C,A,U */ + 260 310 260 280 /* UA,GU,C,C,A */ + 260 310 260 280 /* UA,GU,C,C,C */ + 260 310 260 280 /* UA,GU,C,C,G */ + 260 310 260 280 /* UA,GU,C,C,U */ + 220 330 220 300 /* UA,GU,C,G,A */ + 260 310 260 280 /* UA,GU,C,G,C */ + 130 180 130 150 /* UA,GU,C,G,G */ + 260 310 260 280 /* UA,GU,C,G,U */ + 260 310 260 280 /* UA,GU,C,U,A */ + 260 310 260 280 /* UA,GU,C,U,C */ + 260 310 260 280 /* UA,GU,C,U,G */ + 260 310 260 280 /* UA,GU,C,U,U */ + 240 340 190 340 /* UA,GU,G,A,A */ + 200 310 150 310 /* UA,GU,G,A,C */ + 120 230 200 230 /* UA,GU,G,A,G */ + 200 310 150 310 /* UA,GU,G,A,U */ + 200 310 150 310 /* UA,GU,G,C,A */ + 260 310 150 310 /* UA,GU,G,C,C */ + 200 310 150 310 /* UA,GU,G,C,G */ + 260 310 150 310 /* UA,GU,G,C,U */ + 160 270 240 270 /* UA,GU,G,G,A */ + 200 310 150 310 /* UA,GU,G,G,C */ + 200 180 280 180 /* UA,GU,G,G,G */ + 200 310 150 310 /* UA,GU,G,G,U */ + 200 310 150 310 /* UA,GU,G,U,A */ + 260 310 150 310 /* UA,GU,G,U,C */ + 200 310 150 310 /* UA,GU,G,U,G */ + 200 310 280 310 /* UA,GU,G,U,U */ + 300 340 300 320 /* UA,GU,U,A,A */ + 260 310 260 220 /* UA,GU,U,A,C */ + 180 290 180 140 /* UA,GU,U,A,G */ + 260 310 260 220 /* UA,GU,U,A,U */ + 260 310 260 220 /* UA,GU,U,C,A */ + 260 310 260 220 /* UA,GU,U,C,C */ + 260 310 260 220 /* UA,GU,U,C,G */ + 260 310 260 220 /* UA,GU,U,C,U */ + 220 330 220 180 /* UA,GU,U,G,A */ + 260 310 260 220 /* UA,GU,U,G,C */ + 130 180 130 220 /* UA,GU,U,G,G */ + 260 310 260 220 /* UA,GU,U,G,U */ + 260 310 260 220 /* UA,GU,U,U,A */ + 260 310 260 220 /* UA,GU,U,U,C */ + 260 310 260 220 /* UA,GU,U,U,G */ + 260 310 260 220 /* UA,GU,U,U,U */ + 240 240 150 240 /* UA,UG,A,A,A */ + 280 280 180 280 /* UA,UG,A,A,C */ + 140 140 50 140 /* UA,UG,A,A,G */ + 280 280 180 280 /* UA,UG,A,A,U */ + 280 280 180 280 /* UA,UG,A,C,A */ + 280 280 240 280 /* UA,UG,A,C,C */ + 280 280 180 280 /* UA,UG,A,C,G */ + 280 280 240 280 /* UA,UG,A,C,U */ + 310 310 210 310 /* UA,UG,A,G,A */ + 280 280 180 280 /* UA,UG,A,G,C */ + 150 150 180 150 /* UA,UG,A,G,G */ + 280 280 180 280 /* UA,UG,A,G,U */ + 280 280 180 280 /* UA,UG,A,U,A */ + 280 280 240 280 /* UA,UG,A,U,C */ + 280 280 180 280 /* UA,UG,A,U,G */ + 340 280 180 280 /* UA,UG,A,U,U */ + 200 240 200 210 /* UA,UG,C,A,A */ + 230 280 230 250 /* UA,UG,C,A,C */ + 100 200 100 170 /* UA,UG,C,A,G */ + 230 280 230 250 /* UA,UG,C,A,U */ + 230 280 230 250 /* UA,UG,C,C,A */ + 230 280 230 250 /* UA,UG,C,C,C */ + 230 280 230 250 /* UA,UG,C,C,G */ + 230 280 230 250 /* UA,UG,C,C,U */ + 260 370 260 340 /* UA,UG,C,G,A */ + 230 280 230 250 /* UA,UG,C,G,C */ + 100 150 100 120 /* UA,UG,C,G,G */ + 230 280 230 250 /* UA,UG,C,G,U */ + 230 280 230 250 /* UA,UG,C,U,A */ + 230 280 230 250 /* UA,UG,C,U,C */ + 230 280 230 250 /* UA,UG,C,U,G */ + 230 280 230 250 /* UA,UG,C,U,U */ + 140 240 90 240 /* UA,UG,G,A,A */ + 170 280 120 280 /* UA,UG,G,A,C */ + 40 140 120 140 /* UA,UG,G,A,G */ + 170 280 120 280 /* UA,UG,G,A,U */ + 170 280 120 280 /* UA,UG,G,C,A */ + 230 280 120 280 /* UA,UG,G,C,C */ + 170 280 120 280 /* UA,UG,G,C,G */ + 230 280 120 280 /* UA,UG,G,C,U */ + 200 310 280 310 /* UA,UG,G,G,A */ + 170 280 120 280 /* UA,UG,G,G,C */ + 170 150 250 150 /* UA,UG,G,G,G */ + 170 280 120 280 /* UA,UG,G,G,U */ + 170 280 120 280 /* UA,UG,G,U,A */ + 230 280 120 280 /* UA,UG,G,U,C */ + 170 280 120 280 /* UA,UG,G,U,G */ + 170 280 250 280 /* UA,UG,G,U,U */ + 200 240 200 220 /* UA,UG,U,A,A */ + 230 280 230 190 /* UA,UG,U,A,C */ + 100 200 100 60 /* UA,UG,U,A,G */ + 230 280 230 190 /* UA,UG,U,A,U */ + 230 280 230 190 /* UA,UG,U,C,A */ + 230 280 230 190 /* UA,UG,U,C,C */ + 230 280 230 190 /* UA,UG,U,C,G */ + 230 280 230 190 /* UA,UG,U,C,U */ + 260 370 260 220 /* UA,UG,U,G,A */ + 230 280 230 190 /* UA,UG,U,G,C */ + 100 150 100 190 /* UA,UG,U,G,G */ + 230 280 230 190 /* UA,UG,U,G,U */ + 230 280 230 190 /* UA,UG,U,U,A */ + 230 280 230 190 /* UA,UG,U,U,C */ + 230 280 230 190 /* UA,UG,U,U,G */ + 230 280 230 190 /* UA,UG,U,U,U */ + 280 280 180 280 /* UA,AU,A,A,A */ + 250 250 160 250 /* UA,AU,A,A,C */ + 150 150 60 150 /* UA,AU,A,A,G */ + 250 250 160 250 /* UA,AU,A,A,U */ + 260 260 170 260 /* UA,AU,A,C,A */ + 260 260 220 260 /* UA,AU,A,C,C */ + 260 260 170 260 /* UA,AU,A,C,G */ + 260 260 220 260 /* UA,AU,A,C,U */ + 220 220 130 220 /* UA,AU,A,G,A */ + 250 250 160 250 /* UA,AU,A,G,C */ + 100 100 140 100 /* UA,AU,A,G,G */ + 250 250 160 250 /* UA,AU,A,G,U */ + 260 260 170 260 /* UA,AU,A,U,A */ + 260 260 220 260 /* UA,AU,A,U,C */ + 260 260 170 260 /* UA,AU,A,U,G */ + 230 170 70 170 /* UA,AU,A,U,U */ + 230 280 230 250 /* UA,AU,C,A,A */ + 210 250 210 220 /* UA,AU,C,A,C */ + 110 210 110 180 /* UA,AU,C,A,G */ + 210 250 210 220 /* UA,AU,C,A,U */ + 220 260 220 230 /* UA,AU,C,C,A */ + 210 260 210 230 /* UA,AU,C,C,C */ + 220 260 220 230 /* UA,AU,C,C,G */ + 210 260 210 230 /* UA,AU,C,C,U */ + 180 280 180 250 /* UA,AU,C,G,A */ + 210 250 210 220 /* UA,AU,C,G,C */ + 60 100 60 70 /* UA,AU,C,G,G */ + 210 250 210 220 /* UA,AU,C,G,U */ + 220 260 220 230 /* UA,AU,C,U,A */ + 210 260 210 230 /* UA,AU,C,U,C */ + 220 260 220 230 /* UA,AU,C,U,G */ + 120 170 120 140 /* UA,AU,C,U,U */ + 170 280 120 280 /* UA,AU,G,A,A */ + 150 250 100 250 /* UA,AU,G,A,C */ + 50 150 130 150 /* UA,AU,G,A,G */ + 150 250 100 250 /* UA,AU,G,A,U */ + 160 260 110 260 /* UA,AU,G,C,A */ + 210 260 100 260 /* UA,AU,G,C,C */ + 160 260 110 260 /* UA,AU,G,C,G */ + 210 260 100 260 /* UA,AU,G,C,U */ + 120 220 200 220 /* UA,AU,G,G,A */ + 150 250 100 250 /* UA,AU,G,G,C */ + 130 100 210 100 /* UA,AU,G,G,G */ + 150 250 100 250 /* UA,AU,G,G,U */ + 160 260 110 260 /* UA,AU,G,U,A */ + 210 260 100 260 /* UA,AU,G,U,C */ + 160 260 110 260 /* UA,AU,G,U,G */ + 60 170 140 170 /* UA,AU,G,U,U */ + 230 280 230 250 /* UA,AU,U,A,A */ + 210 250 210 170 /* UA,AU,U,A,C */ + 110 210 110 70 /* UA,AU,U,A,G */ + 210 250 210 170 /* UA,AU,U,A,U */ + 220 260 220 180 /* UA,AU,U,C,A */ + 210 260 210 170 /* UA,AU,U,C,C */ + 220 260 220 180 /* UA,AU,U,C,G */ + 210 260 210 170 /* UA,AU,U,C,U */ + 180 280 180 140 /* UA,AU,U,G,A */ + 210 250 210 170 /* UA,AU,U,G,C */ + 60 100 60 150 /* UA,AU,U,G,G */ + 210 250 210 170 /* UA,AU,U,G,U */ + 220 260 220 180 /* UA,AU,U,U,A */ + 210 260 210 170 /* UA,AU,U,U,C */ + 220 260 220 180 /* UA,AU,U,U,G */ + 120 170 120 80 /* UA,AU,U,U,U */ + 280 280 180 280 /* UA,UA,A,A,A */ + 230 230 140 230 /* UA,UA,A,A,C */ + 170 170 80 170 /* UA,UA,A,A,G */ + 230 230 140 230 /* UA,UA,A,A,U */ + 280 280 180 280 /* UA,UA,A,C,A */ + 280 280 240 280 /* UA,UA,A,C,C */ + 280 280 180 280 /* UA,UA,A,C,G */ + 280 280 240 280 /* UA,UA,A,C,U */ + 180 180 90 180 /* UA,UA,A,G,A */ + 230 230 140 230 /* UA,UA,A,G,C */ + 120 120 160 120 /* UA,UA,A,G,G */ + 230 230 140 230 /* UA,UA,A,G,U */ + 280 280 180 280 /* UA,UA,A,U,A */ + 250 250 210 250 /* UA,UA,A,U,C */ + 280 280 180 280 /* UA,UA,A,U,G */ + 250 190 100 190 /* UA,UA,A,U,U */ + 230 280 230 250 /* UA,UA,C,A,A */ + 190 230 190 200 /* UA,UA,C,A,C */ + 130 230 130 200 /* UA,UA,C,A,G */ + 190 230 190 200 /* UA,UA,C,A,U */ + 230 280 230 250 /* UA,UA,C,C,A */ + 230 280 230 250 /* UA,UA,C,C,C */ + 230 280 230 250 /* UA,UA,C,C,G */ + 230 280 230 250 /* UA,UA,C,C,U */ + 140 240 140 210 /* UA,UA,C,G,A */ + 190 230 190 200 /* UA,UA,C,G,C */ + 80 120 80 90 /* UA,UA,C,G,G */ + 190 230 190 200 /* UA,UA,C,G,U */ + 230 280 230 250 /* UA,UA,C,U,A */ + 200 250 200 220 /* UA,UA,C,U,C */ + 230 280 230 250 /* UA,UA,C,U,G */ + 150 190 150 160 /* UA,UA,C,U,U */ + 170 280 120 280 /* UA,UA,G,A,A */ + 130 230 80 230 /* UA,UA,G,A,C */ + 70 170 150 170 /* UA,UA,G,A,G */ + 130 230 80 230 /* UA,UA,G,A,U */ + 170 280 120 280 /* UA,UA,G,C,A */ + 230 280 120 280 /* UA,UA,G,C,C */ + 170 280 120 280 /* UA,UA,G,C,G */ + 230 280 120 280 /* UA,UA,G,C,U */ + 80 180 160 180 /* UA,UA,G,G,A */ + 130 230 80 230 /* UA,UA,G,G,C */ + 150 120 230 120 /* UA,UA,G,G,G */ + 130 230 80 230 /* UA,UA,G,G,U */ + 170 280 120 280 /* UA,UA,G,U,A */ + 200 250 90 250 /* UA,UA,G,U,C */ + 170 280 120 280 /* UA,UA,G,U,G */ + 90 190 170 190 /* UA,UA,G,U,U */ + 230 280 230 250 /* UA,UA,U,A,A */ + 190 230 190 150 /* UA,UA,U,A,C */ + 130 230 130 90 /* UA,UA,U,A,G */ + 190 230 190 150 /* UA,UA,U,A,U */ + 230 280 230 190 /* UA,UA,U,C,A */ + 230 280 230 190 /* UA,UA,U,C,C */ + 230 280 230 190 /* UA,UA,U,C,G */ + 230 280 230 190 /* UA,UA,U,C,U */ + 140 240 140 100 /* UA,UA,U,G,A */ + 190 230 190 150 /* UA,UA,U,G,C */ + 80 120 80 170 /* UA,UA,U,G,G */ + 190 230 190 150 /* UA,UA,U,G,U */ + 230 280 230 190 /* UA,UA,U,U,A */ + 200 250 200 160 /* UA,UA,U,U,C */ + 230 280 230 190 /* UA,UA,U,U,G */ + 150 190 150 110 /* UA,UA,U,U,U */ + +# int22_enthalpies + -460 -310 -960 -310 /* CG,CG,A,A,A */ + -770 -620 -1270 -620 /* CG,CG,A,A,C */ + -670 -530 -1170 -530 /* CG,CG,A,A,G */ + -770 -620 -1270 -620 /* CG,CG,A,A,U */ + -310 -170 -810 -170 /* CG,CG,A,C,A */ + -320 -170 -580 -170 /* CG,CG,A,C,C */ + -310 -170 -810 -170 /* CG,CG,A,C,G */ + -370 -220 -630 -220 /* CG,CG,A,C,U */ + -960 -810 -1460 -810 /* CG,CG,A,G,A */ + -770 -620 -1270 -620 /* CG,CG,A,G,C */ + -120 30 -1870 30 /* CG,CG,A,G,G */ + -770 -620 -1270 -620 /* CG,CG,A,G,U */ + -310 -170 -810 -170 /* CG,CG,A,U,A */ + -260 -110 -520 -110 /* CG,CG,A,U,C */ + -310 -170 -810 -170 /* CG,CG,A,U,G */ + -860 -960 -1600 -960 /* CG,CG,A,U,U */ + -770 -320 -770 -260 /* CG,CG,C,A,A */ + -1080 -630 -1080 -570 /* CG,CG,C,A,C */ + -980 -290 -980 -230 /* CG,CG,C,A,G */ + -1080 -630 -1080 -570 /* CG,CG,C,A,U */ + -620 -170 -620 -110 /* CG,CG,C,C,A */ + -630 -180 -630 -120 /* CG,CG,C,C,C */ + -620 -170 -620 -110 /* CG,CG,C,C,G */ + -680 -230 -680 -170 /* CG,CG,C,C,U */ + -1270 -580 -1270 -520 /* CG,CG,C,G,A */ + -1080 -630 -1080 -570 /* CG,CG,C,G,C */ + -430 20 -430 80 /* CG,CG,C,G,G */ + -1080 -630 -1080 -570 /* CG,CG,C,G,U */ + -620 -170 -620 -110 /* CG,CG,C,U,A */ + -570 -120 -570 -60 /* CG,CG,C,U,C */ + -620 -170 -620 -110 /* CG,CG,C,U,G */ + -1410 -960 -1410 -900 /* CG,CG,C,U,U */ + -670 -310 -120 -310 /* CG,CG,G,A,A */ + -980 -620 -430 -620 /* CG,CG,G,A,C */ + -890 -530 -1580 -530 /* CG,CG,G,A,G */ + -980 -620 -430 -620 /* CG,CG,G,A,U */ + -530 -170 30 -170 /* CG,CG,G,C,A */ + -290 -170 20 -170 /* CG,CG,G,C,C */ + -530 -170 30 -170 /* CG,CG,G,C,G */ + -340 -220 -30 -220 /* CG,CG,G,C,U */ + -1170 -810 -1870 -810 /* CG,CG,G,G,A */ + -980 -620 -430 -620 /* CG,CG,G,G,C */ + -1580 30 -2280 30 /* CG,CG,G,G,G */ + -980 -620 -430 -620 /* CG,CG,G,G,U */ + -530 -170 30 -170 /* CG,CG,G,U,A */ + -230 -110 80 -110 /* CG,CG,G,U,C */ + -530 -170 30 -170 /* CG,CG,G,U,G */ + -1320 -960 -2010 -960 /* CG,CG,G,U,U */ + -770 -370 -770 -860 /* CG,CG,U,A,A */ + -1080 -680 -1080 -1410 /* CG,CG,U,A,C */ + -980 -340 -980 -1320 /* CG,CG,U,A,G */ + -1080 -680 -1080 -1410 /* CG,CG,U,A,U */ + -620 -220 -620 -960 /* CG,CG,U,C,A */ + -630 -230 -630 -960 /* CG,CG,U,C,C */ + -620 -220 -620 -960 /* CG,CG,U,C,G */ + -680 -280 -680 -1010 /* CG,CG,U,C,U */ + -1270 -630 -1270 -1600 /* CG,CG,U,G,A */ + -1080 -680 -1080 -1410 /* CG,CG,U,G,C */ + -430 -30 -430 -2010 /* CG,CG,U,G,G */ + -1080 -680 -1080 -1410 /* CG,CG,U,G,U */ + -620 -220 -620 -960 /* CG,CG,U,U,A */ + -570 -170 -570 -900 /* CG,CG,U,U,C */ + -620 -220 -620 -960 /* CG,CG,U,U,G */ + -1410 -1010 -1410 -1750 /* CG,CG,U,U,U */ + -580 -220 -970 -150 /* CG,GC,A,A,A */ + -740 -600 -100 -600 /* CG,GC,A,A,C */ + -2010 -1650 -1980 -1340 /* CG,GC,A,A,G */ + -740 -600 -1240 -600 /* CG,GC,A,A,U */ + -660 -1150 10 -510 /* CG,GC,A,C,A */ + -960 -820 540 -820 /* CG,GC,A,C,C */ + -660 -510 -1160 -510 /* CG,GC,A,C,G */ + -960 -820 -1220 -820 /* CG,GC,A,C,U */ + -1340 -860 -2450 -860 /* CG,GC,A,G,A */ + -740 -600 -1240 -600 /* CG,GC,A,G,C */ + 180 -390 -1870 30 /* CG,GC,A,G,G */ + -740 -600 -1240 -600 /* CG,GC,A,G,U */ + -660 -510 -1160 -510 /* CG,GC,A,U,A */ + -1270 -1130 -1530 -1130 /* CG,GC,A,U,C */ + -660 -510 -1160 -510 /* CG,GC,A,U,G */ + -1240 -90 -810 -800 /* CG,GC,A,U,U */ + -600 -1070 -600 -90 /* CG,GC,C,A,A */ + -1050 -600 -1050 -540 /* CG,GC,C,A,C */ + -1790 -630 -1790 -1040 /* CG,GC,C,A,G */ + -1050 -600 -1050 -540 /* CG,GC,C,A,U */ + -970 -750 -970 -460 /* CG,GC,C,C,A */ + -1270 -820 -1270 -760 /* CG,GC,C,C,C */ + -970 -520 -970 -460 /* CG,GC,C,C,G */ + -1270 -820 -1270 -550 /* CG,GC,C,C,U */ + -1070 -500 -1320 -570 /* CG,GC,C,G,A */ + -1050 -600 -1050 -540 /* CG,GC,C,G,C */ + -430 20 -430 180 /* CG,GC,C,G,G */ + -1050 -600 -1050 -540 /* CG,GC,C,G,U */ + -970 -520 -970 -460 /* CG,GC,C,U,A */ + -1580 -1130 -1580 -1070 /* CG,GC,C,U,C */ + -970 -520 -970 -460 /* CG,GC,C,U,G */ + -830 -1710 -1260 -1460 /* CG,GC,C,U,U */ + -1600 -150 -200 -150 /* CG,GC,G,A,A */ + -350 -600 -440 -600 /* CG,GC,G,A,C */ + -3070 -1340 -2390 -1340 /* CG,GC,G,A,G */ + -960 -600 -400 -600 /* CG,GC,G,A,U */ + -1110 -510 -320 -510 /* CG,GC,G,C,A */ + -940 -820 -620 -820 /* CG,GC,G,C,C */ + -870 -510 -320 -510 /* CG,GC,G,C,G */ + -940 -820 -260 -820 /* CG,GC,G,C,U */ + -1880 -860 -1080 -860 /* CG,GC,G,G,A */ + -960 -600 -400 -600 /* CG,GC,G,G,C */ + -1370 30 -2280 30 /* CG,GC,G,G,G */ + -960 -600 -400 -600 /* CG,GC,G,G,U */ + -870 -510 -320 -510 /* CG,GC,G,U,A */ + -1250 -1130 -210 -1130 /* CG,GC,G,U,C */ + -870 -510 -320 -510 /* CG,GC,G,U,G */ + -1360 -800 -1550 -800 /* CG,GC,G,U,U */ + -600 -200 -600 -1490 /* CG,GC,U,A,A */ + -1050 -650 -1050 -1390 /* CG,GC,U,A,C */ + -1790 -1150 -1790 -1520 /* CG,GC,U,A,G */ + -1050 -650 -1050 -1390 /* CG,GC,U,A,U */ + -970 -570 -970 -400 /* CG,GC,U,C,A */ + -1270 -870 -1270 -1610 /* CG,GC,U,C,C */ + -970 -570 -970 -1300 /* CG,GC,U,C,G */ + -1270 -870 -1270 -1610 /* CG,GC,U,C,U */ + -1320 -1750 -1320 -1300 /* CG,GC,U,G,A */ + -1050 -650 -1050 -1390 /* CG,GC,U,G,C */ + -430 -880 -430 -230 /* CG,GC,U,G,G */ + -1050 -650 -1050 -1390 /* CG,GC,U,G,U */ + -970 -570 -970 -1300 /* CG,GC,U,U,A */ + -1580 -1180 -1580 -1920 /* CG,GC,U,U,C */ + -970 -570 -970 -1300 /* CG,GC,U,U,G */ + -1260 -860 -1260 -2350 /* CG,GC,U,U,U */ + -1370 -1240 -1890 -1240 /* CG,GU,A,A,A */ + -1210 -1060 -1710 -1060 /* CG,GU,A,A,C */ + -1220 -1080 -1720 -1080 /* CG,GU,A,A,G */ + -1210 -1060 -1710 -1060 /* CG,GU,A,A,U */ + -1210 -1060 -1710 -1060 /* CG,GU,A,C,A */ + -1210 -1060 -1470 -1060 /* CG,GU,A,C,C */ + -1210 -1060 -1710 -1060 /* CG,GU,A,C,G */ + -1210 -1060 -1470 -1060 /* CG,GU,A,C,U */ + -1030 -890 -1530 -890 /* CG,GU,A,G,A */ + -1210 -1060 -1710 -1060 /* CG,GU,A,G,C */ + 40 190 -1710 190 /* CG,GU,A,G,G */ + -1210 -1060 -1710 -1060 /* CG,GU,A,G,U */ + -1210 -1060 -1710 -1060 /* CG,GU,A,U,A */ + -1210 -1060 -1470 -1060 /* CG,GU,A,U,C */ + -1210 -1060 -1710 -1060 /* CG,GU,A,U,G */ + -970 -1060 -1710 -1060 /* CG,GU,A,U,U */ + -1700 -1250 -1700 -1190 /* CG,GU,C,A,A */ + -1520 -1070 -1520 -1010 /* CG,GU,C,A,C */ + -1530 -840 -1530 -780 /* CG,GU,C,A,G */ + -1520 -1070 -1520 -1010 /* CG,GU,C,A,U */ + -1520 -1070 -1520 -1010 /* CG,GU,C,C,A */ + -1520 -1070 -1520 -1010 /* CG,GU,C,C,C */ + -1520 -1070 -1520 -1010 /* CG,GU,C,C,G */ + -1520 -1070 -1520 -1010 /* CG,GU,C,C,U */ + -1340 -650 -1340 -590 /* CG,GU,C,G,A */ + -1520 -1070 -1520 -1010 /* CG,GU,C,G,C */ + -270 180 -270 240 /* CG,GU,C,G,G */ + -1520 -1070 -1520 -1010 /* CG,GU,C,G,U */ + -1520 -1070 -1520 -1010 /* CG,GU,C,U,A */ + -1520 -1070 -1520 -1010 /* CG,GU,C,U,C */ + -1520 -1070 -1520 -1010 /* CG,GU,C,U,G */ + -1520 -1070 -1520 -1010 /* CG,GU,C,U,U */ + -1600 -1240 -1050 -1240 /* CG,GU,G,A,A */ + -1420 -1060 -870 -1060 /* CG,GU,G,A,C */ + -1440 -1080 -2130 -1080 /* CG,GU,G,A,G */ + -1420 -1060 -870 -1060 /* CG,GU,G,A,U */ + -1420 -1060 -870 -1060 /* CG,GU,G,C,A */ + -1180 -1060 -870 -1060 /* CG,GU,G,C,C */ + -1420 -1060 -870 -1060 /* CG,GU,G,C,G */ + -1180 -1060 -870 -1060 /* CG,GU,G,C,U */ + -1250 -890 -1940 -890 /* CG,GU,G,G,A */ + -1420 -1060 -870 -1060 /* CG,GU,G,G,C */ + -1420 190 -2120 190 /* CG,GU,G,G,G */ + -1420 -1060 -870 -1060 /* CG,GU,G,G,U */ + -1420 -1060 -870 -1060 /* CG,GU,G,U,A */ + -1180 -1060 -870 -1060 /* CG,GU,G,U,C */ + -1420 -1060 -870 -1060 /* CG,GU,G,U,G */ + -1420 -1060 -2120 -1060 /* CG,GU,G,U,U */ + -1700 -1300 -1700 -1790 /* CG,GU,U,A,A */ + -1520 -1120 -1520 -1850 /* CG,GU,U,A,C */ + -1530 -890 -1530 -1870 /* CG,GU,U,A,G */ + -1520 -1120 -1520 -1850 /* CG,GU,U,A,U */ + -1520 -1120 -1520 -1850 /* CG,GU,U,C,A */ + -1520 -1120 -1520 -1850 /* CG,GU,U,C,C */ + -1520 -1120 -1520 -1850 /* CG,GU,U,C,G */ + -1520 -1120 -1520 -1850 /* CG,GU,U,C,U */ + -1340 -700 -1340 -1680 /* CG,GU,U,G,A */ + -1520 -1120 -1520 -1850 /* CG,GU,U,G,C */ + -270 130 -270 -1850 /* CG,GU,U,G,G */ + -1520 -1120 -1520 -1850 /* CG,GU,U,G,U */ + -1520 -1120 -1520 -1850 /* CG,GU,U,U,A */ + -1520 -1120 -1520 -1850 /* CG,GU,U,U,C */ + -1520 -1120 -1520 -1850 /* CG,GU,U,U,G */ + -1520 -1120 -1520 -1850 /* CG,GU,U,U,U */ + -140 0 -640 0 /* CG,UG,A,A,A */ + -650 -510 -1150 -510 /* CG,UG,A,A,C */ + -990 -850 -1490 -850 /* CG,UG,A,A,G */ + -650 -510 -1150 -510 /* CG,UG,A,A,U */ + -650 -510 -1150 -510 /* CG,UG,A,C,A */ + -650 -510 -910 -510 /* CG,UG,A,C,C */ + -650 -510 -1150 -510 /* CG,UG,A,C,G */ + -650 -510 -910 -510 /* CG,UG,A,C,U */ + -1160 -1020 -1660 -1020 /* CG,UG,A,G,A */ + -650 -510 -1150 -510 /* CG,UG,A,G,C */ + 600 740 -1150 740 /* CG,UG,A,G,G */ + -650 -510 -1150 -510 /* CG,UG,A,G,U */ + -650 -510 -1150 -510 /* CG,UG,A,U,A */ + -650 -510 -910 -510 /* CG,UG,A,U,C */ + -650 -510 -1150 -510 /* CG,UG,A,U,G */ + -410 -510 -1150 -510 /* CG,UG,A,U,U */ + -450 0 -450 50 /* CG,UG,C,A,A */ + -960 -510 -960 -450 /* CG,UG,C,A,C */ + -1300 -610 -1300 -550 /* CG,UG,C,A,G */ + -960 -510 -960 -450 /* CG,UG,C,A,U */ + -960 -510 -960 -450 /* CG,UG,C,C,A */ + -960 -510 -960 -450 /* CG,UG,C,C,C */ + -960 -510 -960 -450 /* CG,UG,C,C,G */ + -960 -510 -960 -450 /* CG,UG,C,C,U */ + -1470 -780 -1470 -720 /* CG,UG,C,G,A */ + -960 -510 -960 -450 /* CG,UG,C,G,C */ + 290 740 290 800 /* CG,UG,C,G,G */ + -960 -510 -960 -450 /* CG,UG,C,G,U */ + -960 -510 -960 -450 /* CG,UG,C,U,A */ + -960 -510 -960 -450 /* CG,UG,C,U,C */ + -960 -510 -960 -450 /* CG,UG,C,U,G */ + -960 -510 -960 -450 /* CG,UG,C,U,U */ + -360 0 200 0 /* CG,UG,G,A,A */ + -870 -510 -310 -510 /* CG,UG,G,A,C */ + -1210 -850 -1900 -850 /* CG,UG,G,A,G */ + -870 -510 -310 -510 /* CG,UG,G,A,U */ + -870 -510 -310 -510 /* CG,UG,G,C,A */ + -630 -510 -310 -510 /* CG,UG,G,C,C */ + -870 -510 -310 -510 /* CG,UG,G,C,G */ + -630 -510 -310 -510 /* CG,UG,G,C,U */ + -1380 -1020 -2070 -1020 /* CG,UG,G,G,A */ + -870 -510 -310 -510 /* CG,UG,G,G,C */ + -870 740 -1560 740 /* CG,UG,G,G,G */ + -870 -510 -310 -510 /* CG,UG,G,G,U */ + -870 -510 -310 -510 /* CG,UG,G,U,A */ + -630 -510 -310 -510 /* CG,UG,G,U,C */ + -870 -510 -310 -510 /* CG,UG,G,U,G */ + -870 -510 -1560 -510 /* CG,UG,G,U,U */ + -450 -50 -450 -550 /* CG,UG,U,A,A */ + -960 -560 -960 -1300 /* CG,UG,U,A,C */ + -1300 -660 -1300 -1640 /* CG,UG,U,A,G */ + -960 -560 -960 -1300 /* CG,UG,U,A,U */ + -960 -560 -960 -1300 /* CG,UG,U,C,A */ + -960 -560 -960 -1300 /* CG,UG,U,C,C */ + -960 -560 -960 -1300 /* CG,UG,U,C,G */ + -960 -560 -960 -1300 /* CG,UG,U,C,U */ + -1470 -830 -1470 -1810 /* CG,UG,U,G,A */ + -960 -560 -960 -1300 /* CG,UG,U,G,C */ + 290 690 290 -1300 /* CG,UG,U,G,G */ + -960 -560 -960 -1300 /* CG,UG,U,G,U */ + -960 -560 -960 -1300 /* CG,UG,U,U,A */ + -960 -560 -960 -1300 /* CG,UG,U,U,C */ + -960 -560 -960 -1300 /* CG,UG,U,U,G */ + -960 -560 -960 -1300 /* CG,UG,U,U,U */ + 440 580 -60 580 /* CG,AU,A,A,A */ + 130 270 -370 270 /* CG,AU,A,A,C */ + -950 -800 -1450 -800 /* CG,AU,A,A,G */ + 130 270 -370 270 /* CG,AU,A,A,U */ + 140 290 -350 290 /* CG,AU,A,C,A */ + 140 280 -120 280 /* CG,AU,A,C,C */ + 140 290 -350 290 /* CG,AU,A,C,G */ + 140 280 -120 280 /* CG,AU,A,C,U */ + -770 -620 -1270 -620 /* CG,AU,A,G,A */ + 130 270 -370 270 /* CG,AU,A,G,C */ + 970 1120 -780 1120 /* CG,AU,A,G,G */ + 130 270 -370 270 /* CG,AU,A,G,U */ + 140 290 -350 290 /* CG,AU,A,U,A */ + 140 280 -120 280 /* CG,AU,A,U,C */ + 140 290 -350 290 /* CG,AU,A,U,G */ + -600 -690 -1340 -690 /* CG,AU,A,U,U */ + 130 580 130 640 /* CG,AU,C,A,A */ + -180 270 -180 330 /* CG,AU,C,A,C */ + -1260 -570 -1260 -510 /* CG,AU,C,A,G */ + -180 270 -180 330 /* CG,AU,C,A,U */ + -160 280 -160 340 /* CG,AU,C,C,A */ + -170 280 -170 340 /* CG,AU,C,C,C */ + -160 280 -160 340 /* CG,AU,C,C,G */ + -170 280 -170 340 /* CG,AU,C,C,U */ + -1080 -390 -1080 -330 /* CG,AU,C,G,A */ + -180 270 -180 330 /* CG,AU,C,G,C */ + 660 1110 660 1170 /* CG,AU,C,G,G */ + -180 270 -180 330 /* CG,AU,C,G,U */ + -160 280 -160 340 /* CG,AU,C,U,A */ + -170 280 -170 340 /* CG,AU,C,U,C */ + -160 280 -160 340 /* CG,AU,C,U,G */ + -1150 -700 -1150 -640 /* CG,AU,C,U,U */ + 220 580 780 580 /* CG,AU,G,A,A */ + -80 270 470 270 /* CG,AU,G,A,C */ + -1160 -800 -1860 -800 /* CG,AU,G,A,G */ + -80 270 470 270 /* CG,AU,G,A,U */ + -70 290 490 290 /* CG,AU,G,C,A */ + 170 280 480 280 /* CG,AU,G,C,C */ + -70 290 490 290 /* CG,AU,G,C,G */ + 170 280 480 280 /* CG,AU,G,C,U */ + -980 -620 -1680 -620 /* CG,AU,G,G,A */ + -80 270 470 270 /* CG,AU,G,G,C */ + -490 1120 -1190 1120 /* CG,AU,G,G,G */ + -80 270 470 270 /* CG,AU,G,G,U */ + -70 290 490 290 /* CG,AU,G,U,A */ + 170 280 480 280 /* CG,AU,G,U,C */ + -70 290 490 290 /* CG,AU,G,U,G */ + -1050 -690 -1750 -690 /* CG,AU,G,U,U */ + 130 530 130 40 /* CG,AU,U,A,A */ + -180 220 -180 -510 /* CG,AU,U,A,C */ + -1260 -620 -1260 -1590 /* CG,AU,U,A,G */ + -180 220 -180 -510 /* CG,AU,U,A,U */ + -160 230 -160 -500 /* CG,AU,U,C,A */ + -170 230 -170 -500 /* CG,AU,U,C,C */ + -160 230 -160 -500 /* CG,AU,U,C,G */ + -170 230 -170 -500 /* CG,AU,U,C,U */ + -1080 -440 -1080 -1410 /* CG,AU,U,G,A */ + -180 220 -180 -510 /* CG,AU,U,G,C */ + 660 1060 660 -920 /* CG,AU,U,G,G */ + -180 220 -180 -510 /* CG,AU,U,G,U */ + -160 230 -160 -500 /* CG,AU,U,U,A */ + -170 230 -170 -500 /* CG,AU,U,U,C */ + -160 230 -160 -500 /* CG,AU,U,U,G */ + -1150 -750 -1150 -1480 /* CG,AU,U,U,U */ + 500 650 0 650 /* CG,UA,A,A,A */ + 220 370 -270 370 /* CG,UA,A,A,C */ + -900 -750 -1400 -750 /* CG,UA,A,A,G */ + 220 370 -270 370 /* CG,UA,A,A,U */ + 370 520 -120 520 /* CG,UA,A,C,A */ + 370 520 120 520 /* CG,UA,A,C,C */ + 370 520 -120 520 /* CG,UA,A,C,G */ + 240 390 -10 390 /* CG,UA,A,C,U */ + -1200 -1050 -1700 -1050 /* CG,UA,A,G,A */ + 220 370 -270 370 /* CG,UA,A,G,C */ + 1160 1300 -590 1300 /* CG,UA,A,G,G */ + 220 370 -270 370 /* CG,UA,A,G,U */ + 370 520 -120 520 /* CG,UA,A,U,A */ + -60 80 -320 80 /* CG,UA,A,U,C */ + 370 520 -120 520 /* CG,UA,A,U,G */ + -320 -420 -1060 -420 /* CG,UA,A,U,U */ + 190 640 190 700 /* CG,UA,C,A,A */ + -80 360 -80 420 /* CG,UA,C,A,C */ + -1210 -520 -1210 -460 /* CG,UA,C,A,G */ + -80 360 -80 420 /* CG,UA,C,A,U */ + 60 510 60 570 /* CG,UA,C,C,A */ + 60 510 60 570 /* CG,UA,C,C,C */ + 60 510 60 570 /* CG,UA,C,C,G */ + -60 380 -60 440 /* CG,UA,C,C,U */ + -1510 -820 -1510 -760 /* CG,UA,C,G,A */ + -80 360 -80 420 /* CG,UA,C,G,C */ + 850 1290 850 1350 /* CG,UA,C,G,G */ + -80 360 -80 420 /* CG,UA,C,G,U */ + 60 510 60 570 /* CG,UA,C,U,A */ + -370 70 -370 130 /* CG,UA,C,U,C */ + 60 510 60 570 /* CG,UA,C,U,G */ + -870 -420 -870 -360 /* CG,UA,C,U,U */ + 290 650 850 650 /* CG,UA,G,A,A */ + 10 370 570 370 /* CG,UA,G,A,C */ + -1110 -750 -1810 -750 /* CG,UA,G,A,G */ + 10 370 570 370 /* CG,UA,G,A,U */ + 160 520 720 520 /* CG,UA,G,C,A */ + 400 520 720 520 /* CG,UA,G,C,C */ + 160 520 720 520 /* CG,UA,G,C,G */ + 270 390 590 390 /* CG,UA,G,C,U */ + -1410 -1050 -2110 -1050 /* CG,UA,G,G,A */ + 10 370 570 370 /* CG,UA,G,G,C */ + -310 1300 -1000 1300 /* CG,UA,G,G,G */ + 10 370 570 370 /* CG,UA,G,G,U */ + 160 520 720 520 /* CG,UA,G,U,A */ + -40 80 280 80 /* CG,UA,G,U,C */ + 160 520 720 520 /* CG,UA,G,U,G */ + -780 -420 -1470 -420 /* CG,UA,G,U,U */ + 190 590 190 100 /* CG,UA,U,A,A */ + -80 310 -80 -420 /* CG,UA,U,A,C */ + -1210 -570 -1210 -1540 /* CG,UA,U,A,G */ + -80 310 -80 -420 /* CG,UA,U,A,U */ + 60 460 60 -270 /* CG,UA,U,C,A */ + 60 460 60 -270 /* CG,UA,U,C,C */ + 60 460 60 -270 /* CG,UA,U,C,G */ + -60 330 -60 -400 /* CG,UA,U,C,U */ + -1510 -870 -1510 -1840 /* CG,UA,U,G,A */ + -80 310 -80 -420 /* CG,UA,U,G,C */ + 850 1250 850 -740 /* CG,UA,U,G,G */ + -80 310 -80 -420 /* CG,UA,U,G,U */ + 60 460 60 -270 /* CG,UA,U,U,A */ + -370 20 -370 -710 /* CG,UA,U,U,C */ + 60 460 60 -270 /* CG,UA,U,U,G */ + -870 -470 -870 -1210 /* CG,UA,U,U,U */ + -580 -660 -1340 -660 /* GC,CG,A,A,A */ + -600 -970 -1070 -970 /* GC,CG,A,A,C */ + -1600 -1110 -1880 -870 /* GC,CG,A,A,G */ + -600 -970 -1320 -970 /* GC,CG,A,A,U */ + -220 -1150 -860 -510 /* GC,CG,A,C,A */ + -1070 -750 -500 -520 /* GC,CG,A,C,C */ + -150 -510 -860 -510 /* GC,CG,A,C,G */ + -200 -570 -1750 -570 /* GC,CG,A,C,U */ + -970 10 -2450 -1160 /* GC,CG,A,G,A */ + -600 -970 -1320 -970 /* GC,CG,A,G,C */ + -200 -320 -1080 -320 /* GC,CG,A,G,G */ + -600 -970 -1320 -970 /* GC,CG,A,G,U */ + -150 -510 -860 -510 /* GC,CG,A,U,A */ + -90 -460 -570 -460 /* GC,CG,A,U,C */ + -150 -510 -860 -510 /* GC,CG,A,U,G */ + -1490 -400 -1300 -1300 /* GC,CG,A,U,U */ + -740 -960 -740 -1270 /* GC,CG,C,A,A */ + -1050 -1270 -1050 -1580 /* GC,CG,C,A,C */ + -350 -940 -960 -1250 /* GC,CG,C,A,G */ + -1050 -1270 -1050 -1580 /* GC,CG,C,A,U */ + -600 -820 -600 -1130 /* GC,CG,C,C,A */ + -600 -820 -600 -1130 /* GC,CG,C,C,C */ + -600 -820 -600 -1130 /* GC,CG,C,C,G */ + -650 -870 -650 -1180 /* GC,CG,C,C,U */ + -100 540 -1240 -1530 /* GC,CG,C,G,A */ + -1050 -1270 -1050 -1580 /* GC,CG,C,G,C */ + -440 -620 -400 -210 /* GC,CG,C,G,G */ + -1050 -1270 -1050 -1580 /* GC,CG,C,G,U */ + -600 -820 -600 -1130 /* GC,CG,C,U,A */ + -540 -760 -540 -1070 /* GC,CG,C,U,C */ + -600 -820 -600 -1130 /* GC,CG,C,U,G */ + -1390 -1610 -1390 -1920 /* GC,CG,C,U,U */ + -2010 -660 180 -660 /* GC,CG,G,A,A */ + -1790 -970 -430 -970 /* GC,CG,G,A,C */ + -3070 -870 -1370 -870 /* GC,CG,G,A,G */ + -1790 -970 -430 -970 /* GC,CG,G,A,U */ + -1650 -510 -390 -510 /* GC,CG,G,C,A */ + -630 -520 20 -520 /* GC,CG,G,C,C */ + -1340 -510 30 -510 /* GC,CG,G,C,G */ + -1150 -570 -880 -570 /* GC,CG,G,C,U */ + -1980 -1160 -1870 -1160 /* GC,CG,G,G,A */ + -1790 -970 -430 -970 /* GC,CG,G,G,C */ + -2390 -320 -2280 -320 /* GC,CG,G,G,G */ + -1790 -970 -430 -970 /* GC,CG,G,G,U */ + -1340 -510 30 -510 /* GC,CG,G,U,A */ + -1040 -460 180 -460 /* GC,CG,G,U,C */ + -1340 -510 30 -510 /* GC,CG,G,U,G */ + -1520 -1300 -230 -1300 /* GC,CG,G,U,U */ + -740 -960 -740 -1240 /* GC,CG,U,A,A */ + -1050 -1270 -1050 -830 /* GC,CG,U,A,C */ + -960 -940 -960 -1360 /* GC,CG,U,A,G */ + -1050 -1270 -1050 -1260 /* GC,CG,U,A,U */ + -600 -820 -600 -90 /* GC,CG,U,C,A */ + -600 -820 -600 -1710 /* GC,CG,U,C,C */ + -600 -820 -600 -800 /* GC,CG,U,C,G */ + -650 -870 -650 -860 /* GC,CG,U,C,U */ + -1240 -1220 -1240 -810 /* GC,CG,U,G,A */ + -1050 -1270 -1050 -1260 /* GC,CG,U,G,C */ + -400 -260 -400 -1550 /* GC,CG,U,G,G */ + -1050 -1270 -1050 -1260 /* GC,CG,U,G,U */ + -600 -820 -600 -800 /* GC,CG,U,U,A */ + -540 -550 -540 -1460 /* GC,CG,U,U,C */ + -600 -820 -600 -800 /* GC,CG,U,U,G */ + -1390 -1610 -1390 -2350 /* GC,CG,U,U,U */ + -130 -490 -840 -490 /* GC,GC,A,A,A */ + -580 -940 -1290 -940 /* GC,GC,A,A,C */ + -1320 -1680 -2030 -1680 /* GC,GC,A,A,G */ + -580 -940 -1290 -940 /* GC,GC,A,A,U */ + -490 -860 -1210 -860 /* GC,GC,A,C,A */ + -800 -1160 -1270 -1160 /* GC,GC,A,C,C */ + -490 -860 -1210 -860 /* GC,GC,A,C,G */ + -800 -1160 -1270 -1160 /* GC,GC,A,C,U */ + -840 -1210 -1560 -1210 /* GC,GC,A,G,A */ + -580 -940 -1290 -940 /* GC,GC,A,G,C */ + 50 -320 -1920 -320 /* GC,GC,A,G,G */ + -580 -940 -1290 -940 /* GC,GC,A,G,U */ + -490 -860 -1210 -860 /* GC,GC,A,U,A */ + -1110 -1470 -1580 -1470 /* GC,GC,A,U,C */ + -490 -860 -1210 -860 /* GC,GC,A,U,G */ + -540 -1150 -1500 -1150 /* GC,GC,A,U,U */ + -580 -800 -580 -1110 /* GC,GC,C,A,A */ + -1030 -1250 -1030 -1560 /* GC,GC,C,A,C */ + -1770 -1750 -1770 -2060 /* GC,GC,C,A,G */ + -1030 -1250 -1030 -1560 /* GC,GC,C,A,U */ + -940 -1160 -940 -1470 /* GC,GC,C,C,A */ + -1250 -1470 -1250 -1780 /* GC,GC,C,C,C */ + -940 -1160 -940 -1470 /* GC,GC,C,C,G */ + -1250 -1470 -1250 -1780 /* GC,GC,C,C,U */ + -1290 -1270 -1290 -1580 /* GC,GC,C,G,A */ + -1030 -1250 -1030 -1560 /* GC,GC,C,G,C */ + -400 -620 -400 -930 /* GC,GC,C,G,G */ + -1030 -1250 -1030 -1560 /* GC,GC,C,G,U */ + -940 -1160 -940 -1470 /* GC,GC,C,U,A */ + -1560 -1780 -1560 -2090 /* GC,GC,C,U,C */ + -940 -1160 -940 -1470 /* GC,GC,C,U,G */ + -1230 -1450 -1230 -1760 /* GC,GC,C,U,U */ + -1320 -490 50 -490 /* GC,GC,G,A,A */ + -1770 -940 -400 -940 /* GC,GC,G,A,C */ + -2510 -1680 -2390 -1680 /* GC,GC,G,A,G */ + -1770 -940 -400 -940 /* GC,GC,G,A,U */ + -1680 -860 -320 -860 /* GC,GC,G,C,A */ + -1750 -1160 -620 -1160 /* GC,GC,G,C,C */ + -1680 -860 -320 -860 /* GC,GC,G,C,G */ + -1750 -1160 -620 -1160 /* GC,GC,G,C,U */ + -2030 -1210 -1920 -1210 /* GC,GC,G,G,A */ + -1770 -940 -400 -940 /* GC,GC,G,G,C */ + -2390 -320 -2280 -320 /* GC,GC,G,G,G */ + -1770 -940 -400 -940 /* GC,GC,G,G,U */ + -1680 -860 -320 -860 /* GC,GC,G,U,A */ + -2060 -1470 -930 -1470 /* GC,GC,G,U,C */ + -1680 -860 -320 -860 /* GC,GC,G,U,G */ + -1970 -1150 -1860 -1150 /* GC,GC,G,U,U */ + -580 -800 -580 -540 /* GC,GC,U,A,A */ + -1030 -1250 -1030 -1230 /* GC,GC,U,A,C */ + -1770 -1750 -1770 -1970 /* GC,GC,U,A,G */ + -1030 -1250 -1030 -1230 /* GC,GC,U,A,U */ + -940 -1160 -940 -1150 /* GC,GC,U,C,A */ + -1250 -1470 -1250 -1450 /* GC,GC,U,C,C */ + -940 -1160 -940 -1150 /* GC,GC,U,C,G */ + -1250 -1470 -1250 -1450 /* GC,GC,U,C,U */ + -1290 -1270 -1290 -1500 /* GC,GC,U,G,A */ + -1030 -1250 -1030 -1230 /* GC,GC,U,G,C */ + -400 -620 -400 -1860 /* GC,GC,U,G,G */ + -1030 -1250 -1030 -1230 /* GC,GC,U,G,U */ + -940 -1160 -940 -1150 /* GC,GC,U,U,A */ + -1560 -1780 -1560 -1760 /* GC,GC,U,U,C */ + -940 -1160 -940 -1150 /* GC,GC,U,U,G */ + -1230 -1450 -1230 -1440 /* GC,GC,U,U,U */ + -1220 -1590 -1940 -1590 /* GC,GU,A,A,A */ + -1040 -1410 -1760 -1410 /* GC,GU,A,A,C */ + -1060 -1420 -1770 -1420 /* GC,GU,A,A,G */ + -1040 -1410 -1760 -1410 /* GC,GU,A,A,U */ + -1040 -1410 -1760 -1410 /* GC,GU,A,C,A */ + -1040 -1410 -1520 -1410 /* GC,GU,A,C,C */ + -1040 -1410 -1760 -1410 /* GC,GU,A,C,G */ + -1040 -1410 -1520 -1410 /* GC,GU,A,C,U */ + -870 -1230 -1580 -1230 /* GC,GU,A,G,A */ + -1040 -1410 -1760 -1410 /* GC,GU,A,G,C */ + 210 -160 -1760 -160 /* GC,GU,A,G,G */ + -1040 -1410 -1760 -1410 /* GC,GU,A,G,U */ + -1040 -1410 -1760 -1410 /* GC,GU,A,U,A */ + -1040 -1410 -1520 -1410 /* GC,GU,A,U,C */ + -1040 -1410 -1760 -1410 /* GC,GU,A,U,G */ + -800 -1410 -1760 -1410 /* GC,GU,A,U,U */ + -1670 -1890 -1670 -2200 /* GC,GU,C,A,A */ + -1490 -1710 -1490 -2020 /* GC,GU,C,A,C */ + -1510 -1490 -1510 -1800 /* GC,GU,C,A,G */ + -1490 -1710 -1490 -2020 /* GC,GU,C,A,U */ + -1490 -1710 -1490 -2020 /* GC,GU,C,C,A */ + -1490 -1710 -1490 -2020 /* GC,GU,C,C,C */ + -1490 -1710 -1490 -2020 /* GC,GU,C,C,G */ + -1490 -1710 -1490 -2020 /* GC,GU,C,C,U */ + -1320 -1300 -1320 -1610 /* GC,GU,C,G,A */ + -1490 -1710 -1490 -2020 /* GC,GU,C,G,C */ + -240 -460 -240 -770 /* GC,GU,C,G,G */ + -1490 -1710 -1490 -2020 /* GC,GU,C,G,U */ + -1490 -1710 -1490 -2020 /* GC,GU,C,U,A */ + -1490 -1710 -1490 -2020 /* GC,GU,C,U,C */ + -1490 -1710 -1490 -2020 /* GC,GU,C,U,G */ + -1490 -1710 -1490 -2020 /* GC,GU,C,U,U */ + -2410 -1590 -1050 -1590 /* GC,GU,G,A,A */ + -2230 -1410 -870 -1410 /* GC,GU,G,A,C */ + -2250 -1420 -2130 -1420 /* GC,GU,G,A,G */ + -2230 -1410 -870 -1410 /* GC,GU,G,A,U */ + -2230 -1410 -870 -1410 /* GC,GU,G,C,A */ + -1990 -1410 -870 -1410 /* GC,GU,G,C,C */ + -2230 -1410 -870 -1410 /* GC,GU,G,C,G */ + -1990 -1410 -870 -1410 /* GC,GU,G,C,U */ + -2060 -1230 -1940 -1230 /* GC,GU,G,G,A */ + -2230 -1410 -870 -1410 /* GC,GU,G,G,C */ + -2230 -160 -2120 -160 /* GC,GU,G,G,G */ + -2230 -1410 -870 -1410 /* GC,GU,G,G,U */ + -2230 -1410 -870 -1410 /* GC,GU,G,U,A */ + -1990 -1410 -870 -1410 /* GC,GU,G,U,C */ + -2230 -1410 -870 -1410 /* GC,GU,G,U,G */ + -2230 -1410 -2120 -1410 /* GC,GU,G,U,U */ + -1670 -1890 -1670 -1640 /* GC,GU,U,A,A */ + -1490 -1710 -1490 -1700 /* GC,GU,U,A,C */ + -1510 -1490 -1510 -1710 /* GC,GU,U,A,G */ + -1490 -1710 -1490 -1700 /* GC,GU,U,A,U */ + -1490 -1710 -1490 -1700 /* GC,GU,U,C,A */ + -1490 -1710 -1490 -1700 /* GC,GU,U,C,C */ + -1490 -1710 -1490 -1700 /* GC,GU,U,C,G */ + -1490 -1710 -1490 -1700 /* GC,GU,U,C,U */ + -1320 -1300 -1320 -1520 /* GC,GU,U,G,A */ + -1490 -1710 -1490 -1700 /* GC,GU,U,G,C */ + -240 -460 -240 -1700 /* GC,GU,U,G,G */ + -1490 -1710 -1490 -1700 /* GC,GU,U,G,U */ + -1490 -1710 -1490 -1700 /* GC,GU,U,U,A */ + -1490 -1710 -1490 -1700 /* GC,GU,U,U,C */ + -1490 -1710 -1490 -1700 /* GC,GU,U,U,G */ + -1490 -1710 -1490 -1700 /* GC,GU,U,U,U */ + -2040 -340 -690 -340 /* GC,UG,A,A,A */ + -490 -850 -1200 -850 /* GC,UG,A,A,C */ + -830 -1190 -1540 -1190 /* GC,UG,A,A,G */ + -490 -850 -1200 -850 /* GC,UG,A,A,U */ + -490 -850 -1200 -850 /* GC,UG,A,C,A */ + -490 -850 -960 -850 /* GC,UG,A,C,C */ + -490 -850 -1200 -850 /* GC,UG,A,C,G */ + -490 -850 -960 -850 /* GC,UG,A,C,U */ + -1000 -1360 -1710 -1360 /* GC,UG,A,G,A */ + -490 -850 -1200 -850 /* GC,UG,A,G,C */ + 760 400 -1200 400 /* GC,UG,A,G,G */ + -490 -850 -1200 -850 /* GC,UG,A,G,U */ + -490 -850 -1200 -850 /* GC,UG,A,U,A */ + -490 -850 -960 -850 /* GC,UG,A,U,C */ + -490 -850 -1200 -850 /* GC,UG,A,U,G */ + -250 -850 -1200 -850 /* GC,UG,A,U,U */ + -430 -650 -430 -960 /* GC,UG,C,A,A */ + -940 -1160 -940 -1470 /* GC,UG,C,A,C */ + -1280 -1260 -1280 -1570 /* GC,UG,C,A,G */ + -940 -1160 -940 -1470 /* GC,UG,C,A,U */ + -940 -1160 -940 -1470 /* GC,UG,C,C,A */ + -940 -1160 -940 -1470 /* GC,UG,C,C,C */ + -940 -1160 -940 -1470 /* GC,UG,C,C,G */ + -940 -1160 -940 -1470 /* GC,UG,C,C,U */ + -1450 -1430 -1450 -1740 /* GC,UG,C,G,A */ + -940 -1160 -940 -1470 /* GC,UG,C,G,C */ + 310 90 310 -220 /* GC,UG,C,G,G */ + -940 -1160 -940 -1470 /* GC,UG,C,G,U */ + -940 -1160 -940 -1470 /* GC,UG,C,U,A */ + -940 -1160 -940 -1470 /* GC,UG,C,U,C */ + -940 -1160 -940 -1470 /* GC,UG,C,U,G */ + -940 -1160 -940 -1470 /* GC,UG,C,U,U */ + -1170 -340 200 -340 /* GC,UG,G,A,A */ + -1680 -850 -310 -850 /* GC,UG,G,A,C */ + -2020 -1190 -1900 -1190 /* GC,UG,G,A,G */ + -1680 -850 -310 -850 /* GC,UG,G,A,U */ + -1680 -850 -310 -850 /* GC,UG,G,C,A */ + -1440 -850 -310 -850 /* GC,UG,G,C,C */ + -1680 -850 -310 -850 /* GC,UG,G,C,G */ + -1440 -850 -310 -850 /* GC,UG,G,C,U */ + -2190 -1360 -2070 -1360 /* GC,UG,G,G,A */ + -1680 -850 -310 -850 /* GC,UG,G,G,C */ + -1680 400 -1560 400 /* GC,UG,G,G,G */ + -1680 -850 -310 -850 /* GC,UG,G,G,U */ + -1680 -850 -310 -850 /* GC,UG,G,U,A */ + -1440 -850 -310 -850 /* GC,UG,G,U,C */ + -1680 -850 -310 -850 /* GC,UG,G,U,G */ + -1680 -850 -1560 -850 /* GC,UG,G,U,U */ + -430 -650 -430 -390 /* GC,UG,U,A,A */ + -940 -1160 -940 -1140 /* GC,UG,U,A,C */ + -1280 -1260 -1280 -1480 /* GC,UG,U,A,G */ + -940 -1160 -940 -1140 /* GC,UG,U,A,U */ + -940 -1160 -940 -1140 /* GC,UG,U,C,A */ + -940 -1160 -940 -1140 /* GC,UG,U,C,C */ + -940 -1160 -940 -1140 /* GC,UG,U,C,G */ + -940 -1160 -940 -1140 /* GC,UG,U,C,U */ + -1450 -1430 -1450 -1650 /* GC,UG,U,G,A */ + -940 -1160 -940 -1140 /* GC,UG,U,G,C */ + 310 90 310 -1140 /* GC,UG,U,G,G */ + -940 -1160 -940 -1140 /* GC,UG,U,G,U */ + -940 -1160 -940 -1140 /* GC,UG,U,U,A */ + -940 -1160 -940 -1140 /* GC,UG,U,U,C */ + -940 -1160 -940 -1140 /* GC,UG,U,U,G */ + -940 -1160 -940 -1140 /* GC,UG,U,U,U */ + 600 240 -110 240 /* GC,AU,A,A,A */ + 290 -70 -420 -70 /* GC,AU,A,A,C */ + -780 -1150 -1500 -1150 /* GC,AU,A,A,G */ + 290 -70 -420 -70 /* GC,AU,A,A,U */ + 310 -50 -400 -50 /* GC,AU,A,C,A */ + 300 -60 -170 -60 /* GC,AU,A,C,C */ + 310 -50 -400 -50 /* GC,AU,A,C,G */ + 300 -60 -170 -60 /* GC,AU,A,C,U */ + -600 -970 -1320 -970 /* GC,AU,A,G,A */ + 290 -70 -420 -70 /* GC,AU,A,G,C */ + 1140 770 -830 770 /* GC,AU,A,G,G */ + 290 -70 -420 -70 /* GC,AU,A,G,U */ + 310 -50 -400 -50 /* GC,AU,A,U,A */ + 300 -60 -170 -60 /* GC,AU,A,U,C */ + 310 -50 -400 -50 /* GC,AU,A,U,G */ + -430 -1040 -1390 -1040 /* GC,AU,A,U,U */ + 150 -60 150 -370 /* GC,AU,C,A,A */ + -150 -370 -150 -680 /* GC,AU,C,A,C */ + -1230 -1210 -1230 -1520 /* GC,AU,C,A,G */ + -150 -370 -150 -680 /* GC,AU,C,A,U */ + -140 -360 -140 -670 /* GC,AU,C,C,A */ + -140 -360 -140 -670 /* GC,AU,C,C,C */ + -140 -360 -140 -670 /* GC,AU,C,C,G */ + -140 -360 -140 -670 /* GC,AU,C,C,U */ + -1050 -1030 -1050 -1340 /* GC,AU,C,G,A */ + -150 -370 -150 -680 /* GC,AU,C,G,C */ + 690 470 690 160 /* GC,AU,C,G,G */ + -150 -370 -150 -680 /* GC,AU,C,G,U */ + -140 -360 -140 -670 /* GC,AU,C,U,A */ + -140 -360 -140 -670 /* GC,AU,C,U,C */ + -140 -360 -140 -670 /* GC,AU,C,U,G */ + -1120 -1340 -1120 -1650 /* GC,AU,C,U,U */ + -580 240 780 240 /* GC,AU,G,A,A */ + -890 -70 470 -70 /* GC,AU,G,A,C */ + -1970 -1150 -1860 -1150 /* GC,AU,G,A,G */ + -890 -70 470 -70 /* GC,AU,G,A,U */ + -880 -50 490 -50 /* GC,AU,G,C,A */ + -640 -60 480 -60 /* GC,AU,G,C,C */ + -880 -50 490 -50 /* GC,AU,G,C,G */ + -640 -60 480 -60 /* GC,AU,G,C,U */ + -1790 -970 -1680 -970 /* GC,AU,G,G,A */ + -890 -70 470 -70 /* GC,AU,G,G,C */ + -1300 770 -1190 770 /* GC,AU,G,G,G */ + -890 -70 470 -70 /* GC,AU,G,G,U */ + -880 -50 490 -50 /* GC,AU,G,U,A */ + -640 -60 480 -60 /* GC,AU,G,U,C */ + -880 -50 490 -50 /* GC,AU,G,U,G */ + -1860 -1040 -1750 -1040 /* GC,AU,G,U,U */ + 150 -60 150 190 /* GC,AU,U,A,A */ + -150 -370 -150 -360 /* GC,AU,U,A,C */ + -1230 -1210 -1230 -1440 /* GC,AU,U,A,G */ + -150 -370 -150 -360 /* GC,AU,U,A,U */ + -140 -360 -140 -340 /* GC,AU,U,C,A */ + -140 -360 -140 -350 /* GC,AU,U,C,C */ + -140 -360 -140 -340 /* GC,AU,U,C,G */ + -140 -360 -140 -350 /* GC,AU,U,C,U */ + -1050 -1030 -1050 -1260 /* GC,AU,U,G,A */ + -150 -370 -150 -360 /* GC,AU,U,G,C */ + 690 470 690 -770 /* GC,AU,U,G,G */ + -150 -370 -150 -360 /* GC,AU,U,G,U */ + -140 -360 -140 -340 /* GC,AU,U,U,A */ + -140 -360 -140 -350 /* GC,AU,U,U,C */ + -140 -360 -140 -340 /* GC,AU,U,U,G */ + -1120 -1340 -1120 -1330 /* GC,AU,U,U,U */ + 670 300 -40 300 /* GC,UA,A,A,A */ + 390 20 -320 20 /* GC,UA,A,A,C */ + -730 -1100 -1450 -1100 /* GC,UA,A,A,G */ + 390 20 -320 20 /* GC,UA,A,A,U */ + 540 170 -170 170 /* GC,UA,A,C,A */ + 540 170 70 170 /* GC,UA,A,C,C */ + 540 170 -170 170 /* GC,UA,A,C,G */ + 410 40 -60 40 /* GC,UA,A,C,U */ + -1030 -1400 -1750 -1400 /* GC,UA,A,G,A */ + 390 20 -320 20 /* GC,UA,A,G,C */ + 1320 960 -640 960 /* GC,UA,A,G,G */ + 390 20 -320 20 /* GC,UA,A,G,U */ + 540 170 -170 170 /* GC,UA,A,U,A */ + 100 -260 -370 -260 /* GC,UA,A,U,C */ + 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GU,GU,G,A,G */ + -1970 -1960 -710 -1960 /* GU,GU,G,A,U */ + -1970 -1960 -710 -1960 /* GU,GU,G,C,A */ + -1730 -1960 -710 -1960 /* GU,GU,G,C,C */ + -1970 -1960 -710 -1960 /* GU,GU,G,C,G */ + -1730 -1960 -710 -1960 /* GU,GU,G,C,U */ + -1800 -1780 -1780 -1780 /* GU,GU,G,G,A */ + -1970 -1960 -710 -1960 /* GU,GU,G,G,C */ + -1970 -710 -1960 -710 /* GU,GU,G,G,G */ + -1970 -1960 -710 -1960 /* GU,GU,G,G,U */ + -1970 -1960 -710 -1960 /* GU,GU,G,U,A */ + -1730 -1960 -710 -1960 /* GU,GU,G,U,C */ + -1970 -1960 -710 -1960 /* GU,GU,G,U,G */ + -1970 -1960 -1960 -1960 /* GU,GU,G,U,U */ + -2140 -2140 -2140 -1900 /* GU,GU,U,A,A */ + -1960 -1960 -1960 -1960 /* GU,GU,U,A,C */ + -1970 -1730 -1970 -1970 /* GU,GU,U,A,G */ + -1960 -1960 -1960 -1960 /* GU,GU,U,A,U */ + -1960 -1960 -1960 -1960 /* GU,GU,U,C,A */ + -1960 -1960 -1960 -1960 /* GU,GU,U,C,C */ + -1960 -1960 -1960 -1960 /* GU,GU,U,C,G */ + -1960 -1960 -1960 -1960 /* GU,GU,U,C,U */ + -1780 -1540 -1780 -1780 /* GU,GU,U,G,A */ + -1960 -1960 -1960 -1960 /* GU,GU,U,G,C */ + -710 -710 -710 -1960 /* GU,GU,U,G,G */ + -1960 -1960 -1960 -1960 /* GU,GU,U,G,U */ + -1960 -1960 -1960 -1960 /* GU,GU,U,U,A */ + -1960 -1960 -1960 -1960 /* GU,GU,U,U,C */ + -1960 -1960 -1960 -1960 /* GU,GU,U,U,G */ + -1960 -1960 -1960 -1960 /* GU,GU,U,U,U */ + -70 -890 -30 -890 /* GU,UG,A,A,A */ + -1580 -1400 -1230 -1400 /* GU,UG,A,A,C */ + -1600 -1740 -1570 -1740 /* GU,UG,A,A,G */ + -1580 -1400 -1230 -1400 /* GU,UG,A,A,U */ + -1580 -1400 -1230 -1400 /* GU,UG,A,C,A */ + -1580 -1400 -990 -1400 /* GU,UG,A,C,C */ + -1580 -1400 -1230 -1400 /* GU,UG,A,C,G */ + -1580 -1400 -990 -1400 /* GU,UG,A,C,U */ + -2090 -1910 -1740 -1910 /* GU,UG,A,G,A */ + -1580 -1400 -1230 -1400 /* GU,UG,A,G,C */ + -330 -150 -1230 -150 /* GU,UG,A,G,G */ + -1580 -1400 -1230 -1400 /* GU,UG,A,G,U */ + -1580 -1400 -1230 -1400 /* GU,UG,A,U,A */ + -1580 -1400 -990 -1400 /* GU,UG,A,U,C */ + -1580 -1400 -1230 -1400 /* GU,UG,A,U,G */ + -1340 -1400 -1230 -1400 /* GU,UG,A,U,U */ + -890 -890 -890 -890 /* GU,UG,C,A,A */ + -1400 -1400 -1400 -1400 /* GU,UG,C,A,C */ + -1740 -1500 -1740 -1500 /* GU,UG,C,A,G */ + -1400 -1400 -1400 -1400 /* GU,UG,C,A,U */ + -1400 -1400 -1400 -1400 /* GU,UG,C,C,A */ + -1400 -1400 -1400 -1400 /* GU,UG,C,C,C */ + -1400 -1400 -1400 -1400 /* GU,UG,C,C,G */ + -1400 -1400 -1400 -1400 /* GU,UG,C,C,U */ + -1910 -1670 -1910 -1670 /* GU,UG,C,G,A */ + -1400 -1400 -1400 -1400 /* GU,UG,C,G,C */ + -150 -150 -150 -150 /* GU,UG,C,G,G */ + -1400 -1400 -1400 -1400 /* GU,UG,C,G,U */ + -1400 -1400 -1400 -1400 /* GU,UG,C,U,A */ + -1400 -1400 -1400 -1400 /* GU,UG,C,U,C */ + -1400 -1400 -1400 -1400 /* GU,UG,C,U,G */ + -1400 -1400 -1400 -1400 /* GU,UG,C,U,U */ + -910 -890 360 -890 /* GU,UG,G,A,A */ + -1420 -1400 -150 -1400 /* GU,UG,G,A,C */ + -3040 -1740 -1740 -1740 /* GU,UG,G,A,G */ + -1420 -1400 -150 -1400 /* GU,UG,G,A,U */ + -1420 -1400 -150 -1400 /* GU,UG,G,C,A */ + -1180 -1400 -150 -1400 /* GU,UG,G,C,C */ + -1420 -1400 -150 -1400 /* GU,UG,G,C,G */ + -1180 -1400 -150 -1400 /* GU,UG,G,C,U */ + -1930 -1910 -1910 -1910 /* GU,UG,G,G,A */ + -1420 -1400 -150 -1400 /* GU,UG,G,G,C */ + -1420 -150 -1400 -150 /* GU,UG,G,G,G */ + -1420 -1400 -150 -1400 /* GU,UG,G,G,U */ + -1420 -1400 -150 -1400 /* GU,UG,G,U,A */ + -1180 -1400 -150 -1400 /* GU,UG,G,U,C */ + -1420 -1400 -150 -1400 /* GU,UG,G,U,G */ + -1420 -1400 -1400 -1400 /* GU,UG,G,U,U */ + -890 -890 -890 -650 /* GU,UG,U,A,A */ + -1400 -1400 -1400 -1400 /* GU,UG,U,A,C */ + -1740 -1500 -1740 -1740 /* GU,UG,U,A,G */ + -1400 -1400 -1400 -1400 /* GU,UG,U,A,U */ + -1400 -1400 -1400 -1400 /* GU,UG,U,C,A */ + -1400 -1400 -1400 -1400 /* GU,UG,U,C,C */ + -1400 -1400 -1400 -1400 /* GU,UG,U,C,G */ + -1400 -1400 -1400 -1400 /* GU,UG,U,C,U */ + -1910 -1670 -1910 -1910 /* GU,UG,U,G,A */ + -1400 -1400 -1400 -1400 /* GU,UG,U,G,C */ + -150 -150 -150 -1400 /* GU,UG,U,G,G */ + -1400 -1400 -1400 -1400 /* GU,UG,U,G,U */ + -1400 -1400 -1400 -1400 /* GU,UG,U,U,A */ + -1400 -1400 -1400 -1400 /* GU,UG,U,U,C */ + -1400 -1400 -1400 -1400 /* GU,UG,U,U,G */ + -1400 -1400 -1400 -1400 /* GU,UG,U,U,U */ + -490 -310 -130 -310 /* GU,AU,A,A,A */ + -800 -620 -440 -620 /* GU,AU,A,A,C */ + -1880 -1700 -1520 -1700 /* GU,AU,A,A,G */ + -800 -620 -440 -620 /* GU,AU,A,A,U */ + -780 -600 -430 -600 /* GU,AU,A,C,A */ + -790 -610 -190 -610 /* GU,AU,A,C,C */ + -780 -600 -430 -600 /* GU,AU,A,C,G */ + -790 -610 -190 -610 /* GU,AU,A,C,U */ + -1700 -1520 -1340 -1520 /* GU,AU,A,G,A */ + -800 -620 -440 -620 /* GU,AU,A,G,C */ + 40 220 -850 220 /* GU,AU,A,G,G */ + -800 -620 -440 -620 /* GU,AU,A,G,U */ + -780 -600 -430 -600 /* GU,AU,A,U,A */ + -790 -610 -190 -610 /* GU,AU,A,U,C */ + -780 -600 -430 -600 /* GU,AU,A,U,G */ + -1530 -1590 -1410 -1590 /* GU,AU,A,U,U */ + -310 -310 -310 -310 /* GU,AU,C,A,A */ + -620 -620 -620 -620 /* GU,AU,C,A,C */ + -1700 -1460 -1700 -1460 /* GU,AU,C,A,G */ + -620 -620 -620 -620 /* GU,AU,C,A,U */ + -600 -600 -600 -600 /* GU,AU,C,C,A */ + -610 -610 -610 -610 /* GU,AU,C,C,C */ + -600 -600 -600 -600 /* GU,AU,C,C,G */ + -610 -610 -610 -610 /* GU,AU,C,C,U */ + -1520 -1280 -1520 -1280 /* GU,AU,C,G,A */ + -620 -620 -620 -620 /* GU,AU,C,G,C */ + 220 220 220 220 /* GU,AU,C,G,G */ + -620 -620 -620 -620 /* GU,AU,C,G,U */ + -600 -600 -600 -600 /* GU,AU,C,U,A */ + -610 -610 -610 -610 /* GU,AU,C,U,C */ + -600 -600 -600 -600 /* GU,AU,C,U,G */ + -1590 -1590 -1590 -1590 /* GU,AU,C,U,U */ + -320 -310 940 -310 /* GU,AU,G,A,A */ + -630 -620 630 -620 /* GU,AU,G,A,C */ + -1710 -1700 -1700 -1700 /* GU,AU,G,A,G */ + -630 -620 630 -620 /* GU,AU,G,A,U */ + -620 -600 650 -600 /* GU,AU,G,C,A */ + -380 -610 640 -610 /* GU,AU,G,C,C */ + -620 -600 650 -600 /* GU,AU,G,C,G */ + -380 -610 640 -610 /* GU,AU,G,C,U */ + -1530 -1520 -1520 -1520 /* GU,AU,G,G,A */ + -630 -620 630 -620 /* GU,AU,G,G,C */ + -1040 220 -1030 220 /* GU,AU,G,G,G */ + -630 -620 630 -620 /* GU,AU,G,G,U */ + -620 -600 650 -600 /* GU,AU,G,U,A */ + -380 -610 640 -610 /* GU,AU,G,U,C */ + -620 -600 650 -600 /* GU,AU,G,U,G */ + -1600 -1590 -1590 -1590 /* GU,AU,G,U,U */ + -310 -310 -310 -70 /* GU,AU,U,A,A */ + -620 -620 -620 -620 /* GU,AU,U,A,C */ + -1700 -1460 -1700 -1700 /* GU,AU,U,A,G */ + -620 -620 -620 -620 /* GU,AU,U,A,U */ + -600 -600 -600 -600 /* GU,AU,U,C,A */ + -610 -610 -610 -610 /* GU,AU,U,C,C */ + -600 -600 -600 -600 /* GU,AU,U,C,G */ + -610 -610 -610 -610 /* GU,AU,U,C,U */ + -1520 -1280 -1520 -1520 /* GU,AU,U,G,A */ + -620 -620 -620 -620 /* GU,AU,U,G,C */ + 220 220 220 -1030 /* GU,AU,U,G,G */ + -620 -620 -620 -620 /* GU,AU,U,G,U */ + -600 -600 -600 -600 /* GU,AU,U,U,A */ + -610 -610 -610 -610 /* GU,AU,U,U,C */ + -600 -600 -600 -600 /* GU,AU,U,U,G */ + -1590 -1590 -1590 -1590 /* GU,AU,U,U,U */ + -420 -240 -70 -240 /* GU,UA,A,A,A */ + -700 -520 -350 -520 /* GU,UA,A,A,C */ + -1830 -1650 -1470 -1650 /* GU,UA,A,A,G */ + -700 -520 -350 -520 /* GU,UA,A,A,U */ + -550 -370 -200 -370 /* GU,UA,A,C,A */ + -550 -370 40 -370 /* GU,UA,A,C,C */ + -550 -370 -200 -370 /* GU,UA,A,C,G */ + -680 -500 -90 -500 /* GU,UA,A,C,U */ + -2130 -1950 -1770 -1950 /* GU,UA,A,G,A */ + -700 -520 -350 -520 /* GU,UA,A,G,C */ + 230 410 -670 410 /* GU,UA,A,G,G */ + -700 -520 -350 -520 /* GU,UA,A,G,U */ + -550 -370 -200 -370 /* GU,UA,A,U,A */ + -990 -810 -400 -810 /* GU,UA,A,U,C */ + -550 -370 -200 -370 /* GU,UA,A,U,G */ + -1250 -1310 -1140 -1310 /* GU,UA,A,U,U */ + -240 -240 -240 -240 /* GU,UA,C,A,A */ + -520 -520 -520 -520 /* GU,UA,C,A,C */ + -1650 -1410 -1650 -1410 /* GU,UA,C,A,G */ + -520 -520 -520 -520 /* GU,UA,C,A,U */ + -370 -370 -370 -370 /* GU,UA,C,C,A */ + -370 -370 -370 -370 /* GU,UA,C,C,C */ + -370 -370 -370 -370 /* GU,UA,C,C,G */ + -500 -500 -500 -500 /* GU,UA,C,C,U */ + -1950 -1710 -1950 -1710 /* GU,UA,C,G,A */ + -520 -520 -520 -520 /* GU,UA,C,G,C */ + 410 410 410 410 /* GU,UA,C,G,G */ + -520 -520 -520 -520 /* GU,UA,C,G,U */ + -370 -370 -370 -370 /* GU,UA,C,U,A */ + -810 -810 -810 -810 /* GU,UA,C,U,C */ + -370 -370 -370 -370 /* GU,UA,C,U,G */ + -1310 -1310 -1310 -1310 /* GU,UA,C,U,U */ + -260 -240 1010 -240 /* GU,UA,G,A,A */ + -540 -520 730 -520 /* GU,UA,G,A,C */ + -1660 -1650 -1650 -1650 /* GU,UA,G,A,G */ + -540 -520 730 -520 /* GU,UA,G,A,U */ + -390 -370 880 -370 /* GU,UA,G,C,A */ + -150 -370 880 -370 /* GU,UA,G,C,C */ + -390 -370 880 -370 /* GU,UA,G,C,G */ + -280 -500 750 -500 /* GU,UA,G,C,U */ + -1960 -1950 -1950 -1950 /* GU,UA,G,G,A */ + -540 -520 730 -520 /* GU,UA,G,G,C */ + -860 410 -840 410 /* GU,UA,G,G,G */ + -540 -520 730 -520 /* GU,UA,G,G,U */ + -390 -370 880 -370 /* GU,UA,G,U,A */ + -590 -810 440 -810 /* GU,UA,G,U,C */ + -390 -370 880 -370 /* GU,UA,G,U,G */ + -1330 -1310 -1310 -1310 /* GU,UA,G,U,U */ + -240 -240 -240 0 /* GU,UA,U,A,A */ + -520 -520 -520 -520 /* GU,UA,U,A,C */ + -1650 -1410 -1650 -1650 /* GU,UA,U,A,G */ + -520 -520 -520 -520 /* GU,UA,U,A,U */ + -370 -370 -370 -370 /* GU,UA,U,C,A */ + -370 -370 -370 -370 /* GU,UA,U,C,C */ + -370 -370 -370 -370 /* GU,UA,U,C,G */ + -500 -500 -500 -500 /* GU,UA,U,C,U */ + -1950 -1710 -1950 -1950 /* GU,UA,U,G,A */ + -520 -520 -520 -520 /* GU,UA,U,G,C */ + 410 410 410 -840 /* GU,UA,U,G,G */ + -520 -520 -520 -520 /* GU,UA,U,G,U */ + -370 -370 -370 -370 /* GU,UA,U,U,A */ + -810 -810 -810 -810 /* GU,UA,U,U,C */ + -370 -370 -370 -370 /* GU,UA,U,U,G */ + -1310 -1310 -1310 -1310 /* GU,UA,U,U,U */ + -140 -650 -1160 -650 /* UG,CG,A,A,A */ + -450 -960 -1470 -960 /* UG,CG,A,A,C */ + -360 -870 -1380 -870 /* UG,CG,A,A,G */ + -450 -960 -1470 -960 /* UG,CG,A,A,U */ + 0 -510 -1020 -510 /* UG,CG,A,C,A */ + 0 -510 -780 -510 /* UG,CG,A,C,C */ + 0 -510 -1020 -510 /* UG,CG,A,C,G */ + -50 -560 -830 -560 /* UG,CG,A,C,U */ + -640 -1150 -1660 -1150 /* UG,CG,A,G,A */ + -450 -960 -1470 -960 /* UG,CG,A,G,C */ + 200 -310 -2070 -310 /* UG,CG,A,G,G */ + -450 -960 -1470 -960 /* UG,CG,A,G,U */ + 0 -510 -1020 -510 /* UG,CG,A,U,A */ + 50 -450 -720 -450 /* UG,CG,A,U,C */ + 0 -510 -1020 -510 /* UG,CG,A,U,G */ + -550 -1300 -1810 -1300 /* UG,CG,A,U,U */ + -650 -650 -650 -650 /* UG,CG,C,A,A */ + -960 -960 -960 -960 /* UG,CG,C,A,C */ + -870 -630 -870 -630 /* UG,CG,C,A,G */ + -960 -960 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-850 -510 740 -510 /* UG,CG,G,U,A */ + -550 -450 800 -450 /* UG,CG,G,U,C */ + -850 -510 740 -510 /* UG,CG,G,U,G */ + -1640 -1300 -1300 -1300 /* UG,CG,G,U,U */ + -650 -650 -650 -410 /* UG,CG,U,A,A */ + -960 -960 -960 -960 /* UG,CG,U,A,C */ + -870 -630 -870 -870 /* UG,CG,U,A,G */ + -960 -960 -960 -960 /* UG,CG,U,A,U */ + -510 -510 -510 -510 /* UG,CG,U,C,A */ + -510 -510 -510 -510 /* UG,CG,U,C,C */ + -510 -510 -510 -510 /* UG,CG,U,C,G */ + -560 -560 -560 -560 /* UG,CG,U,C,U */ + -1150 -910 -1150 -1150 /* UG,CG,U,G,A */ + -960 -960 -960 -960 /* UG,CG,U,G,C */ + -310 -310 -310 -1560 /* UG,CG,U,G,G */ + -960 -960 -960 -960 /* UG,CG,U,G,U */ + -510 -510 -510 -510 /* UG,CG,U,U,A */ + -450 -450 -450 -450 /* UG,CG,U,U,C */ + -510 -510 -510 -510 /* UG,CG,U,U,G */ + -1300 -1300 -1300 -1300 /* UG,CG,U,U,U */ + -2040 -490 -1000 -490 /* UG,GC,A,A,A */ + -430 -940 -1450 -940 /* UG,GC,A,A,C */ + -1170 -1680 -2190 -1680 /* UG,GC,A,A,G */ + -430 -940 -1450 -940 /* UG,GC,A,A,U */ + -340 -850 -1360 -850 /* UG,GC,A,C,A */ + -650 -1160 -1430 -1160 /* UG,GC,A,C,C */ + -340 -850 -1360 -850 /* UG,GC,A,C,G */ + -650 -1160 -1430 -1160 /* UG,GC,A,C,U */ + -690 -1200 -1710 -1200 /* UG,GC,A,G,A */ + -430 -940 -1450 -940 /* UG,GC,A,G,C */ + 200 -310 -2070 -310 /* UG,GC,A,G,G */ + -430 -940 -1450 -940 /* UG,GC,A,G,U */ + -340 -850 -1360 -850 /* UG,GC,A,U,A */ + -960 -1470 -1740 -1470 /* UG,GC,A,U,C */ + -340 -850 -1360 -850 /* UG,GC,A,U,G */ + -390 -1140 -1650 -1140 /* UG,GC,A,U,U */ + -490 -490 -490 -490 /* UG,GC,C,A,A */ + -940 -940 -940 -940 /* UG,GC,C,A,C */ + -1680 -1440 -1680 -1440 /* UG,GC,C,A,G */ + -940 -940 -940 -940 /* UG,GC,C,A,U */ + -850 -850 -850 -850 /* UG,GC,C,C,A */ + -1160 -1160 -1160 -1160 /* UG,GC,C,C,C */ + -850 -850 -850 -850 /* UG,GC,C,C,G */ + -1160 -1160 -1160 -1160 /* UG,GC,C,C,U */ + -1200 -960 -1200 -960 /* UG,GC,C,G,A */ + -940 -940 -940 -940 /* UG,GC,C,G,C */ + -310 -310 -310 -310 /* UG,GC,C,G,G */ + -940 -940 -940 -940 /* UG,GC,C,G,U */ + -850 -850 -850 -850 /* UG,GC,C,U,A */ + -1470 -1470 -1470 -1470 /* UG,GC,C,U,C */ + -850 -850 -850 -850 /* UG,GC,C,U,G */ + -1140 -1140 -1140 -1140 /* UG,GC,C,U,U */ + -830 -490 760 -490 /* UG,GC,G,A,A */ + -1280 -940 310 -940 /* UG,GC,G,A,C */ + -2020 -1680 -1680 -1680 /* UG,GC,G,A,G */ + -1280 -940 310 -940 /* UG,GC,G,A,U */ + -1190 -850 400 -850 /* UG,GC,G,C,A */ + -1260 -1160 90 -1160 /* UG,GC,G,C,C */ + -1190 -850 400 -850 /* UG,GC,G,C,G */ + -1260 -1160 90 -1160 /* UG,GC,G,C,U */ + -1540 -1200 -1200 -1200 /* UG,GC,G,G,A */ + -1280 -940 310 -940 /* UG,GC,G,G,C */ + -1900 -310 -1560 -310 /* UG,GC,G,G,G */ + -1280 -940 310 -940 /* UG,GC,G,G,U */ + -1190 -850 400 -850 /* UG,GC,G,U,A */ + -1570 -1470 -220 -1470 /* UG,GC,G,U,C */ + -1190 -850 400 -850 /* UG,GC,G,U,G */ + -1480 -1140 -1140 -1140 /* UG,GC,G,U,U */ + -490 -490 -490 -250 /* UG,GC,U,A,A */ + -940 -940 -940 -940 /* UG,GC,U,A,C */ + -1680 -1440 -1680 -1680 /* UG,GC,U,A,G */ + -940 -940 -940 -940 /* UG,GC,U,A,U */ + -850 -850 -850 -850 /* UG,GC,U,C,A */ + -1160 -1160 -1160 -1160 /* UG,GC,U,C,C */ + -850 -850 -850 -850 /* UG,GC,U,C,G */ + -1160 -1160 -1160 -1160 /* UG,GC,U,C,U */ + -1200 -960 -1200 -1200 /* UG,GC,U,G,A */ + -940 -940 -940 -940 /* UG,GC,U,G,C */ + -310 -310 -310 -1560 /* UG,GC,U,G,G */ + -940 -940 -940 -940 /* UG,GC,U,G,U */ + -850 -850 -850 -850 /* UG,GC,U,U,A */ + -1470 -1470 -1470 -1470 /* UG,GC,U,U,C */ + -850 -850 -850 -850 /* UG,GC,U,U,G */ + -1140 -1140 -1140 -1140 /* UG,GC,U,U,U */ + -70 -1580 -2090 -1580 /* UG,GU,A,A,A */ + -890 -1400 -1910 -1400 /* UG,GU,A,A,C */ + -910 -1420 -1930 -1420 /* UG,GU,A,A,G */ + -890 -1400 -1910 -1400 /* UG,GU,A,A,U */ + -890 -1400 -1910 -1400 /* UG,GU,A,C,A */ + -890 -1400 -1670 -1400 /* UG,GU,A,C,C */ + -890 -1400 -1910 -1400 /* UG,GU,A,C,G */ + -890 -1400 -1670 -1400 /* UG,GU,A,C,U */ + -30 -1230 -1740 -1230 /* UG,GU,A,G,A */ + -890 -1400 -1910 -1400 /* UG,GU,A,G,C */ + 360 -150 -1910 -150 /* UG,GU,A,G,G */ + -890 -1400 -1910 -1400 /* UG,GU,A,G,U */ + -890 -1400 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-150 -1400 /* UG,GU,G,A,U */ + -1740 -1400 -150 -1400 /* UG,GU,G,C,A */ + -1500 -1400 -150 -1400 /* UG,GU,G,C,C */ + -1740 -1400 -150 -1400 /* UG,GU,G,C,G */ + -1500 -1400 -150 -1400 /* UG,GU,G,C,U */ + -1570 -1230 -1230 -1230 /* UG,GU,G,G,A */ + -1740 -1400 -150 -1400 /* UG,GU,G,G,C */ + -1740 -150 -1400 -150 /* UG,GU,G,G,G */ + -1740 -1400 -150 -1400 /* UG,GU,G,G,U */ + -1740 -1400 -150 -1400 /* UG,GU,G,U,A */ + -1500 -1400 -150 -1400 /* UG,GU,G,U,C */ + -1740 -1400 -150 -1400 /* UG,GU,G,U,G */ + -1740 -1400 -1400 -1400 /* UG,GU,G,U,U */ + -1580 -1580 -1580 -1340 /* UG,GU,U,A,A */ + -1400 -1400 -1400 -1400 /* UG,GU,U,A,C */ + -1420 -1180 -1420 -1420 /* UG,GU,U,A,G */ + -1400 -1400 -1400 -1400 /* UG,GU,U,A,U */ + -1400 -1400 -1400 -1400 /* UG,GU,U,C,A */ + -1400 -1400 -1400 -1400 /* UG,GU,U,C,C */ + -1400 -1400 -1400 -1400 /* UG,GU,U,C,G */ + -1400 -1400 -1400 -1400 /* UG,GU,U,C,U */ + -1230 -990 -1230 -1230 /* UG,GU,U,G,A */ + -1400 -1400 -1400 -1400 /* UG,GU,U,G,C */ + -150 -150 -150 -1400 /* UG,GU,U,G,G */ + -1400 -1400 -1400 -1400 /* UG,GU,U,G,U */ + -1400 -1400 -1400 -1400 /* UG,GU,U,U,A */ + -1400 -1400 -1400 -1400 /* UG,GU,U,U,C */ + -1400 -1400 -1400 -1400 /* UG,GU,U,U,G */ + -1400 -1400 -1400 -1400 /* UG,GU,U,U,U */ + 170 -340 -850 -340 /* UG,UG,A,A,A */ + -340 -850 -1360 -850 /* UG,UG,A,A,C */ + -680 -1190 -1700 -1190 /* UG,UG,A,A,G */ + -340 -850 -1360 -850 /* UG,UG,A,A,U */ + -340 -850 -1360 -850 /* UG,UG,A,C,A */ + -340 -850 -1120 -850 /* UG,UG,A,C,C */ + -340 -850 -1360 -850 /* UG,UG,A,C,G */ + -340 -850 -1120 -850 /* UG,UG,A,C,U */ + -850 -1360 -1870 -1360 /* UG,UG,A,G,A */ + -340 -850 -1360 -850 /* UG,UG,A,G,C */ + 910 400 -1360 400 /* UG,UG,A,G,G */ + -340 -850 -1360 -850 /* UG,UG,A,G,U */ + -340 -850 -1360 -850 /* UG,UG,A,U,A */ + -340 -850 -1120 -850 /* UG,UG,A,U,C */ + -340 -850 -1360 -850 /* UG,UG,A,U,G */ + -100 -850 -1360 -850 /* UG,UG,A,U,U */ + -340 -340 -340 -340 /* UG,UG,C,A,A */ + -850 -850 -850 -850 /* UG,UG,C,A,C */ + -1190 -950 -1190 -950 /* UG,UG,C,A,G */ + -850 -850 -850 -850 /* UG,UG,C,A,U */ + -850 -850 -850 -850 /* UG,UG,C,C,A */ + -850 -850 -850 -850 /* UG,UG,C,C,C */ + -850 -850 -850 -850 /* UG,UG,C,C,G */ + -850 -850 -850 -850 /* UG,UG,C,C,U */ + -1360 -1120 -1360 -1120 /* UG,UG,C,G,A */ + -850 -850 -850 -850 /* UG,UG,C,G,C */ + 400 400 400 400 /* UG,UG,C,G,G */ + -850 -850 -850 -850 /* UG,UG,C,G,U */ + -850 -850 -850 -850 /* UG,UG,C,U,A */ + -850 -850 -850 -850 /* UG,UG,C,U,C */ + -850 -850 -850 -850 /* UG,UG,C,U,G */ + -850 -850 -850 -850 /* UG,UG,C,U,U */ + -680 -340 910 -340 /* UG,UG,G,A,A */ + -1190 -850 400 -850 /* UG,UG,G,A,C */ + -1530 -1190 -1190 -1190 /* UG,UG,G,A,G */ + -1190 -850 400 -850 /* UG,UG,G,A,U */ + -1190 -850 400 -850 /* UG,UG,G,C,A */ + -950 -850 400 -850 /* UG,UG,G,C,C */ + -1190 -850 400 -850 /* UG,UG,G,C,G */ + -950 -850 400 -850 /* UG,UG,G,C,U */ + -1700 -1360 -1360 -1360 /* UG,UG,G,G,A */ + -1190 -850 400 -850 /* UG,UG,G,G,C */ + -1190 400 -850 400 /* UG,UG,G,G,G */ + -1190 -850 400 -850 /* UG,UG,G,G,U */ + -1190 -850 400 -850 /* UG,UG,G,U,A */ + -950 -850 400 -850 /* UG,UG,G,U,C */ + -1190 -850 400 -850 /* UG,UG,G,U,G */ + -1190 -850 -850 -850 /* UG,UG,G,U,U */ + -340 -340 -340 -100 /* UG,UG,U,A,A */ + -850 -850 -850 -850 /* UG,UG,U,A,C */ + -1190 -950 -1190 -1190 /* UG,UG,U,A,G */ + -850 -850 -850 -850 /* UG,UG,U,A,U */ + -850 -850 -850 -850 /* UG,UG,U,C,A */ + -850 -850 -850 -850 /* UG,UG,U,C,C */ + -850 -850 -850 -850 /* UG,UG,U,C,G */ + -850 -850 -850 -850 /* UG,UG,U,C,U */ + -1360 -1120 -1360 -1360 /* UG,UG,U,G,A */ + -850 -850 -850 -850 /* UG,UG,U,G,C */ + 400 400 400 -850 /* UG,UG,U,G,G */ + -850 -850 -850 -850 /* UG,UG,U,G,U */ + -850 -850 -850 -850 /* UG,UG,U,U,A */ + -850 -850 -850 -850 /* UG,UG,U,U,C */ + -850 -850 -850 -850 /* UG,UG,U,U,G */ + -850 -850 -850 -850 /* UG,UG,U,U,U */ + 750 240 -260 240 /* UG,AU,A,A,A */ + 440 -60 -570 -60 /* UG,AU,A,A,C */ + -630 -1140 -1650 -1140 /* UG,AU,A,A,G */ + 440 -60 -570 -60 /* UG,AU,A,A,U */ + 460 -50 -560 -50 /* UG,AU,A,C,A */ + 450 -50 -320 -50 /* UG,AU,A,C,C */ + 460 -50 -560 -50 /* UG,AU,A,C,G */ + 450 -50 -320 -50 /* UG,AU,A,C,U */ + -450 -960 -1470 -960 /* UG,AU,A,G,A */ + 440 -60 -570 -60 /* UG,AU,A,G,C */ + 1280 780 -980 780 /* UG,AU,A,G,G */ + 440 -60 -570 -60 /* UG,AU,A,G,U */ + 460 -50 -560 -50 /* UG,AU,A,U,A */ + 450 -50 -320 -50 /* UG,AU,A,U,C */ + 460 -50 -560 -50 /* UG,AU,A,U,G */ + -280 -1030 -1540 -1030 /* UG,AU,A,U,U */ + 240 240 240 240 /* UG,AU,C,A,A */ + -60 -60 -60 -60 /* UG,AU,C,A,C */ + -1140 -900 -1140 -900 /* UG,AU,C,A,G */ + -60 -60 -60 -60 /* UG,AU,C,A,U */ + -50 -50 -50 -50 /* UG,AU,C,C,A */ + -50 -50 -50 -50 /* UG,AU,C,C,C */ + -50 -50 -50 -50 /* UG,AU,C,C,G */ + -50 -50 -50 -50 /* UG,AU,C,C,U */ + -960 -720 -960 -720 /* UG,AU,C,G,A */ + -60 -60 -60 -60 /* UG,AU,C,G,C */ + 780 780 780 780 /* UG,AU,C,G,G */ + -60 -60 -60 -60 /* UG,AU,C,G,U */ + -50 -50 -50 -50 /* UG,AU,C,U,A */ + -50 -50 -50 -50 /* UG,AU,C,U,C */ + -50 -50 -50 -50 /* UG,AU,C,U,G */ + -1030 -1030 -1030 -1030 /* UG,AU,C,U,U */ + -90 240 1490 240 /* UG,AU,G,A,A */ + -400 -60 1190 -60 /* UG,AU,G,A,C */ + -1480 -1140 -1140 -1140 /* UG,AU,G,A,G */ + -400 -60 1190 -60 /* UG,AU,G,A,U */ + -390 -50 1200 -50 /* UG,AU,G,C,A */ + -150 -50 1200 -50 /* UG,AU,G,C,C */ + -390 -50 1200 -50 /* UG,AU,G,C,G */ + -150 -50 1200 -50 /* UG,AU,G,C,U */ + -1300 -960 -960 -960 /* UG,AU,G,G,A */ + -400 -60 1190 -60 /* UG,AU,G,G,C */ + -810 780 -470 780 /* UG,AU,G,G,G */ + -400 -60 1190 -60 /* UG,AU,G,G,U */ + -390 -50 1200 -50 /* UG,AU,G,U,A */ + -150 -50 1200 -50 /* UG,AU,G,U,C */ + -390 -50 1200 -50 /* UG,AU,G,U,G */ + -1370 -1030 -1030 -1030 /* UG,AU,G,U,U */ + 240 240 240 480 /* UG,AU,U,A,A */ + -60 -60 -60 -60 /* UG,AU,U,A,C */ + -1140 -900 -1140 -1140 /* UG,AU,U,A,G */ + -60 -60 -60 -60 /* UG,AU,U,A,U */ + -50 -50 -50 -50 /* UG,AU,U,C,A */ + -50 -50 -50 -50 /* UG,AU,U,C,C */ + -50 -50 -50 -50 /* UG,AU,U,C,G */ + -50 -50 -50 -50 /* UG,AU,U,C,U */ + -960 -720 -960 -960 /* UG,AU,U,G,A */ + -60 -60 -60 -60 /* UG,AU,U,G,C */ + 780 780 780 -470 /* UG,AU,U,G,G */ + -60 -60 -60 -60 /* UG,AU,U,G,U */ + -50 -50 -50 -50 /* UG,AU,U,U,A */ + -50 -50 -50 -50 /* UG,AU,U,U,C */ + -50 -50 -50 -50 /* UG,AU,U,U,G */ + -1030 -1030 -1030 -1030 /* UG,AU,U,U,U */ + 820 310 -200 310 /* UG,UA,A,A,A */ + 540 30 -480 30 /* UG,UA,A,A,C */ + -580 -1090 -1600 -1090 /* UG,UA,A,A,G */ + 540 30 -480 30 /* UG,UA,A,A,U */ + 690 180 -330 180 /* UG,UA,A,C,A */ + 690 180 -90 180 /* UG,UA,A,C,C */ + 690 180 -330 180 /* UG,UA,A,C,G */ + 560 50 -220 50 /* UG,UA,A,C,U */ + -880 -1390 -1900 -1390 /* UG,UA,A,G,A */ + 540 30 -480 30 /* UG,UA,A,G,C */ + 1470 960 -800 960 /* UG,UA,A,G,G */ + 540 30 -480 30 /* UG,UA,A,G,U */ + 690 180 -330 180 /* UG,UA,A,U,A */ + 250 -260 -530 -260 /* UG,UA,A,U,C */ + 690 180 -330 180 /* UG,UA,A,U,G */ + -10 -760 -1270 -760 /* UG,UA,A,U,U */ + 310 310 310 310 /* UG,UA,C,A,A */ + 30 30 30 30 /* UG,UA,C,A,C */ + -1090 -850 -1090 -850 /* UG,UA,C,A,G */ + 30 30 30 30 /* UG,UA,C,A,U */ + 180 180 180 180 /* UG,UA,C,C,A */ + 180 180 180 180 /* UG,UA,C,C,C */ + 180 180 180 180 /* UG,UA,C,C,G */ + 50 50 50 50 /* UG,UA,C,C,U */ + -1390 -1150 -1390 -1150 /* UG,UA,C,G,A */ + 30 30 30 30 /* UG,UA,C,G,C */ + 960 960 960 960 /* UG,UA,C,G,G */ + 30 30 30 30 /* UG,UA,C,G,U */ + 180 180 180 180 /* UG,UA,C,U,A */ + -260 -260 -260 -260 /* UG,UA,C,U,C */ + 180 180 180 180 /* UG,UA,C,U,G */ + -760 -760 -760 -760 /* UG,UA,C,U,U */ + -30 310 1560 310 /* UG,UA,G,A,A */ + -310 30 1280 30 /* UG,UA,G,A,C */ + -1430 -1090 -1090 -1090 /* UG,UA,G,A,G */ + -310 30 1280 30 /* UG,UA,G,A,U */ + -160 180 1430 180 /* UG,UA,G,C,A */ + 80 180 1430 180 /* UG,UA,G,C,C */ + -160 180 1430 180 /* UG,UA,G,C,G */ + -50 50 1300 50 /* UG,UA,G,C,U */ + -1730 -1390 -1390 -1390 /* UG,UA,G,G,A */ + -310 30 1280 30 /* UG,UA,G,G,C */ + -630 960 -290 960 /* UG,UA,G,G,G */ + -310 30 1280 30 /* UG,UA,G,G,U */ + -160 180 1430 180 /* UG,UA,G,U,A */ + -360 -260 990 -260 /* UG,UA,G,U,C */ + -160 180 1430 180 /* UG,UA,G,U,G */ + -1100 -760 -760 -760 /* UG,UA,G,U,U */ + 310 310 310 550 /* UG,UA,U,A,A */ + 30 30 30 30 /* UG,UA,U,A,C */ + -1090 -850 -1090 -1090 /* UG,UA,U,A,G */ + 30 30 30 30 /* UG,UA,U,A,U */ + 180 180 180 180 /* UG,UA,U,C,A */ + 180 180 180 180 /* UG,UA,U,C,C */ + 180 180 180 180 /* UG,UA,U,C,G */ + 50 50 50 50 /* UG,UA,U,C,U */ + -1390 -1150 -1390 -1390 /* UG,UA,U,G,A */ + 30 30 30 30 /* UG,UA,U,G,C */ + 960 960 960 -290 /* UG,UA,U,G,G */ + 30 30 30 30 /* UG,UA,U,G,U */ + 180 180 180 180 /* UG,UA,U,U,A */ + -260 -260 -260 -260 /* UG,UA,U,U,C */ + 180 180 180 180 /* UG,UA,U,U,G */ + -760 -760 -760 -760 /* UG,UA,U,U,U */ + 440 140 -770 140 /* AU,CG,A,A,A */ + 130 -160 -1080 -160 /* AU,CG,A,A,C */ + 220 -70 -980 -70 /* AU,CG,A,A,G */ + 130 -160 -1080 -160 /* AU,CG,A,A,U */ + 580 290 -620 290 /* AU,CG,A,C,A */ + 580 280 -390 280 /* AU,CG,A,C,C */ + 580 290 -620 290 /* AU,CG,A,C,G */ + 530 230 -440 230 /* AU,CG,A,C,U */ + -60 -350 -1270 -350 /* AU,CG,A,G,A */ + 130 -160 -1080 -160 /* AU,CG,A,G,C */ + 780 490 -1680 490 /* AU,CG,A,G,G */ + 130 -160 -1080 -160 /* AU,CG,A,G,U */ + 580 290 -620 290 /* AU,CG,A,U,A */ + 640 340 -330 340 /* AU,CG,A,U,C */ + 580 290 -620 290 /* AU,CG,A,U,G */ + 40 -500 -1410 -500 /* AU,CG,A,U,U */ + 130 140 130 140 /* AU,CG,C,A,A */ + -180 -170 -180 -170 /* AU,CG,C,A,C */ + -80 170 -80 170 /* AU,CG,C,A,G */ + -180 -170 -180 -170 /* AU,CG,C,A,U */ + 270 280 270 280 /* AU,CG,C,C,A */ + 270 280 270 280 /* AU,CG,C,C,C */ + 270 280 270 280 /* AU,CG,C,C,G */ + 220 230 220 230 /* AU,CG,C,C,U */ + -370 -120 -370 -120 /* AU,CG,C,G,A */ + -180 -170 -180 -170 /* AU,CG,C,G,C */ + 470 480 470 480 /* AU,CG,C,G,G */ + -180 -170 -180 -170 /* AU,CG,C,G,U */ + 270 280 270 280 /* AU,CG,C,U,A */ + 330 340 330 340 /* AU,CG,C,U,C */ + 270 280 270 280 /* AU,CG,C,U,G */ + -510 -500 -510 -500 /* AU,CG,C,U,U */ + -950 140 970 140 /* AU,CG,G,A,A */ + -1260 -160 660 -160 /* AU,CG,G,A,C */ + -1160 -70 -490 -70 /* AU,CG,G,A,G */ + -1260 -160 660 -160 /* AU,CG,G,A,U */ + -800 290 1120 290 /* AU,CG,G,C,A */ + -570 280 1110 280 /* AU,CG,G,C,C */ + -800 290 1120 290 /* AU,CG,G,C,G */ + -620 230 1060 230 /* AU,CG,G,C,U */ + -1450 -350 -780 -350 /* AU,CG,G,G,A */ + -1260 -160 660 -160 /* AU,CG,G,G,C */ + -1860 490 -1190 490 /* AU,CG,G,G,G */ + -1260 -160 660 -160 /* AU,CG,G,G,U */ + -800 290 1120 290 /* AU,CG,G,U,A */ + -510 340 1170 340 /* AU,CG,G,U,C */ + -800 290 1120 290 /* AU,CG,G,U,G */ + -1590 -500 -920 -500 /* AU,CG,G,U,U */ + 130 140 130 -600 /* AU,CG,U,A,A */ + -180 -170 -180 -1150 /* AU,CG,U,A,C */ + -80 170 -80 -1050 /* AU,CG,U,A,G */ + -180 -170 -180 -1150 /* AU,CG,U,A,U */ + 270 280 270 -690 /* AU,CG,U,C,A */ + 270 280 270 -700 /* AU,CG,U,C,C */ + 270 280 270 -690 /* AU,CG,U,C,G */ + 220 230 220 -750 /* AU,CG,U,C,U */ + -370 -120 -370 -1340 /* AU,CG,U,G,A */ + -180 -170 -180 -1150 /* AU,CG,U,G,C */ + 470 480 470 -1750 /* AU,CG,U,G,G */ + -180 -170 -180 -1150 /* AU,CG,U,G,U */ + 270 280 270 -690 /* AU,CG,U,U,A */ + 330 340 330 -640 /* AU,CG,U,U,C */ + 270 280 270 -690 /* AU,CG,U,U,G */ + -510 -500 -510 -1480 /* AU,CG,U,U,U */ + 600 310 -600 310 /* AU,GC,A,A,A */ + 150 -140 -1050 -140 /* AU,GC,A,A,C */ + -580 -880 -1790 -880 /* AU,GC,A,A,G */ + 150 -140 -1050 -140 /* AU,GC,A,A,U */ + 240 -50 -970 -50 /* AU,GC,A,C,A */ + -60 -360 -1030 -360 /* AU,GC,A,C,C */ + 240 -50 -970 -50 /* AU,GC,A,C,G */ + -60 -360 -1030 -360 /* AU,GC,A,C,U */ + -110 -400 -1320 -400 /* AU,GC,A,G,A */ + 150 -140 -1050 -140 /* AU,GC,A,G,C */ + 780 490 -1680 490 /* AU,GC,A,G,G */ + 150 -140 -1050 -140 /* AU,GC,A,G,U */ + 240 -50 -970 -50 /* AU,GC,A,U,A */ + -370 -670 -1340 -670 /* AU,GC,A,U,C */ + 240 -50 -970 -50 /* AU,GC,A,U,G */ + 190 -340 -1260 -340 /* AU,GC,A,U,U */ + 290 300 290 300 /* AU,GC,C,A,A */ + -150 -140 -150 -140 /* AU,GC,C,A,C */ + -890 -640 -890 -640 /* AU,GC,C,A,G */ + -150 -140 -150 -140 /* AU,GC,C,A,U */ + -70 -60 -70 -60 /* AU,GC,C,C,A */ + -370 -360 -370 -360 /* AU,GC,C,C,C */ + -70 -60 -70 -60 /* AU,GC,C,C,G */ + -370 -360 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UA,CG,G,G,C */ + -1810 720 -1000 720 /* UA,CG,G,G,G */ + -1210 60 850 60 /* UA,CG,G,G,U */ + -750 520 1300 520 /* UA,CG,G,U,A */ + -460 570 1350 570 /* UA,CG,G,U,C */ + -750 520 1300 520 /* UA,CG,G,U,G */ + -1540 -270 -740 -270 /* UA,CG,G,U,U */ + 220 240 220 -320 /* UA,CG,U,A,A */ + -80 -60 -80 -870 /* UA,CG,U,A,C */ + 10 270 10 -780 /* UA,CG,U,A,G */ + -80 -60 -80 -870 /* UA,CG,U,A,U */ + 370 390 370 -420 /* UA,CG,U,C,A */ + 360 380 360 -420 /* UA,CG,U,C,C */ + 370 390 370 -420 /* UA,CG,U,C,G */ + 310 330 310 -470 /* UA,CG,U,C,U */ + -270 -10 -270 -1060 /* UA,CG,U,G,A */ + -80 -60 -80 -870 /* UA,CG,U,G,C */ + 570 590 570 -1470 /* UA,CG,U,G,G */ + -80 -60 -80 -870 /* UA,CG,U,G,U */ + 370 390 370 -420 /* UA,CG,U,U,A */ + 420 440 420 -360 /* UA,CG,U,U,C */ + 370 390 370 -420 /* UA,CG,U,U,G */ + -420 -400 -420 -1210 /* UA,CG,U,U,U */ + 670 540 -1030 540 /* UA,GC,A,A,A */ + 220 90 -1480 90 /* UA,GC,A,A,C */ + -520 -650 -2220 -650 /* UA,GC,A,A,G */ + 220 90 -1480 90 /* UA,GC,A,A,U */ + 300 170 -1400 170 /* UA,GC,A,C,A */ + 0 -130 -1460 -130 /* UA,GC,A,C,C */ + 300 170 -1400 170 /* UA,GC,A,C,G */ + 0 -130 -1460 -130 /* UA,GC,A,C,U */ + -40 -170 -1750 -170 /* UA,GC,A,G,A */ + 220 90 -1480 90 /* UA,GC,A,G,C */ + 850 720 -2110 720 /* UA,GC,A,G,G */ + 220 90 -1480 90 /* UA,GC,A,G,U */ + 300 170 -1400 170 /* UA,GC,A,U,A */ + -310 -440 -1770 -440 /* UA,GC,A,U,C */ + 300 170 -1400 170 /* UA,GC,A,U,G */ + 250 -110 -1690 -110 /* UA,GC,A,U,U */ + 390 540 390 100 /* UA,GC,C,A,A */ + -60 90 -60 -350 /* UA,GC,C,A,C */ + -800 -410 -800 -850 /* UA,GC,C,A,G */ + -60 90 -60 -350 /* UA,GC,C,A,U */ + 20 170 20 -260 /* UA,GC,C,C,A */ + -280 -130 -280 -570 /* UA,GC,C,C,C */ + 20 170 20 -260 /* UA,GC,C,C,G */ + -280 -130 -280 -570 /* UA,GC,C,C,U */ + -320 70 -320 -370 /* UA,GC,C,G,A */ + -60 90 -60 -350 /* UA,GC,C,G,C */ + 570 720 570 280 /* UA,GC,C,G,G */ + -60 90 -60 -350 /* UA,GC,C,G,U */ + 20 170 20 -260 /* UA,GC,C,U,A */ + -590 -440 -590 -880 /* UA,GC,C,U,C */ + 20 170 20 -260 /* UA,GC,C,U,G */ + -260 -110 -260 -550 /* UA,GC,C,U,U */ + -730 540 1320 540 /* UA,GC,G,A,A */ + -1180 90 870 90 /* UA,GC,G,A,C */ + -1920 -650 -1120 -650 /* UA,GC,G,A,G */ + -1180 90 870 90 /* UA,GC,G,A,U */ + -1100 170 960 170 /* UA,GC,G,C,A */ + -1160 -130 650 -130 /* UA,GC,G,C,C */ + -1100 170 960 170 /* UA,GC,G,C,G */ + -1160 -130 650 -130 /* UA,GC,G,C,U */ + -1450 -170 -640 -170 /* UA,GC,G,G,A */ + -1180 90 870 90 /* UA,GC,G,G,C */ + -1810 720 -1000 720 /* UA,GC,G,G,G */ + -1180 90 870 90 /* UA,GC,G,G,U */ + -1100 170 960 170 /* UA,GC,G,U,A */ + -1470 -440 340 -440 /* UA,GC,G,U,C */ + -1100 170 960 170 /* UA,GC,G,U,G */ + -1390 -110 -580 -110 /* UA,GC,G,U,U */ + 390 410 390 -160 /* UA,GC,U,A,A */ + -60 -40 -60 -850 /* UA,GC,U,A,C */ + -800 -540 -800 -1590 /* UA,GC,U,A,G */ + -60 -40 -60 -850 /* UA,GC,U,A,U */ + 20 40 20 -760 /* UA,GC,U,C,A */ + -280 -260 -280 -1070 /* UA,GC,U,C,C */ + 20 40 20 -760 /* UA,GC,U,C,G */ + -280 -260 -280 -1070 /* UA,GC,U,C,U */ + -320 -60 -320 -1110 /* UA,GC,U,G,A */ + -60 -40 -60 -850 /* UA,GC,U,G,C */ + 570 590 570 -1470 /* UA,GC,U,G,G */ + -60 -40 -60 -850 /* UA,GC,U,G,U */ + 20 40 20 -760 /* UA,GC,U,U,A */ + -590 -570 -590 -1380 /* UA,GC,U,U,C */ + 20 40 20 -760 /* UA,GC,U,U,G */ + -260 -240 -260 -1050 /* UA,GC,U,U,U */ + -420 -550 -2130 -550 /* UA,GU,A,A,A */ + -240 -370 -1950 -370 /* UA,GU,A,A,C */ + -260 -390 -1960 -390 /* UA,GU,A,A,G */ + -240 -370 -1950 -370 /* UA,GU,A,A,U */ + -240 -370 -1950 -370 /* UA,GU,A,C,A */ + -240 -370 -1710 -370 /* UA,GU,A,C,C */ + -240 -370 -1950 -370 /* UA,GU,A,C,G */ + -240 -370 -1710 -370 /* UA,GU,A,C,U */ + -70 -200 -1770 -200 /* UA,GU,A,G,A */ + -240 -370 -1950 -370 /* UA,GU,A,G,C */ + 1010 880 -1950 880 /* UA,GU,A,G,G */ + -240 -370 -1950 -370 /* UA,GU,A,G,U */ + -240 -370 -1950 -370 /* UA,GU,A,U,A */ + -240 -370 -1710 -370 /* UA,GU,A,U,C */ + -240 -370 -1950 -370 /* UA,GU,A,U,G */ + 0 -370 -1950 -370 /* UA,GU,A,U,U */ + -700 -550 -700 -990 /* UA,GU,C,A,A */ + -520 -370 -520 -810 /* UA,GU,C,A,C */ + -540 -150 -540 -590 /* UA,GU,C,A,G */ + -520 -370 -520 -810 /* UA,GU,C,A,U */ + -520 -370 -520 -810 /* UA,GU,C,C,A */ + -520 -370 -520 -810 /* UA,GU,C,C,C */ + -520 -370 -520 -810 /* UA,GU,C,C,G */ + -520 -370 -520 -810 /* UA,GU,C,C,U */ + -350 40 -350 -400 /* UA,GU,C,G,A */ + -520 -370 -520 -810 /* UA,GU,C,G,C */ + 730 880 730 440 /* UA,GU,C,G,G */ + -520 -370 -520 -810 /* UA,GU,C,G,U */ + -520 -370 -520 -810 /* UA,GU,C,U,A */ + -520 -370 -520 -810 /* UA,GU,C,U,C */ + -520 -370 -520 -810 /* UA,GU,C,U,G */ + -520 -370 -520 -810 /* UA,GU,C,U,U */ + -1830 -550 230 -550 /* UA,GU,G,A,A */ + -1650 -370 410 -370 /* UA,GU,G,A,C */ + -1660 -390 -860 -390 /* UA,GU,G,A,G */ + -1650 -370 410 -370 /* UA,GU,G,A,U */ + -1650 -370 410 -370 /* UA,GU,G,C,A */ + -1410 -370 410 -370 /* UA,GU,G,C,C */ + -1650 -370 410 -370 /* UA,GU,G,C,G */ + -1410 -370 410 -370 /* UA,GU,G,C,U */ + -1470 -200 -670 -200 /* UA,GU,G,G,A */ + -1650 -370 410 -370 /* UA,GU,G,G,C */ + -1650 880 -840 880 /* UA,GU,G,G,G */ + -1650 -370 410 -370 /* UA,GU,G,G,U */ + -1650 -370 410 -370 /* UA,GU,G,U,A */ + -1410 -370 410 -370 /* UA,GU,G,U,C */ + -1650 -370 410 -370 /* UA,GU,G,U,G */ + -1650 -370 -840 -370 /* UA,GU,G,U,U */ + -700 -680 -700 -1250 /* UA,GU,U,A,A */ + -520 -500 -520 -1310 /* UA,GU,U,A,C */ + -540 -280 -540 -1330 /* UA,GU,U,A,G */ + -520 -500 -520 -1310 /* UA,GU,U,A,U */ + -520 -500 -520 -1310 /* UA,GU,U,C,A */ + -520 -500 -520 -1310 /* UA,GU,U,C,C */ + -520 -500 -520 -1310 /* UA,GU,U,C,G */ + -520 -500 -520 -1310 /* UA,GU,U,C,U */ + -350 -90 -350 -1140 /* UA,GU,U,G,A */ + -520 -500 -520 -1310 /* UA,GU,U,G,C */ + 730 750 730 -1310 /* UA,GU,U,G,G */ + -520 -500 -520 -1310 /* UA,GU,U,G,U */ + -520 -500 -520 -1310 /* UA,GU,U,U,A */ + -520 -500 -520 -1310 /* UA,GU,U,U,C */ + -520 -500 -520 -1310 /* UA,GU,U,U,G */ + -520 -500 -520 -1310 /* UA,GU,U,U,U */ + 820 690 -880 690 /* UA,UG,A,A,A */ + 310 180 -1390 180 /* UA,UG,A,A,C */ + -30 -160 -1730 -160 /* UA,UG,A,A,G */ + 310 180 -1390 180 /* UA,UG,A,A,U */ + 310 180 -1390 180 /* UA,UG,A,C,A */ + 310 180 -1150 180 /* UA,UG,A,C,C */ + 310 180 -1390 180 /* UA,UG,A,C,G */ + 310 180 -1150 180 /* UA,UG,A,C,U */ + -200 -330 -1900 -330 /* UA,UG,A,G,A */ + 310 180 -1390 180 /* UA,UG,A,G,C */ + 1560 1430 -1390 1430 /* UA,UG,A,G,G */ + 310 180 -1390 180 /* UA,UG,A,G,U */ + 310 180 -1390 180 /* UA,UG,A,U,A */ + 310 180 -1150 180 /* UA,UG,A,U,C */ + 310 180 -1390 180 /* UA,UG,A,U,G */ + 550 180 -1390 180 /* UA,UG,A,U,U */ + 540 690 540 250 /* UA,UG,C,A,A */ + 30 180 30 -260 /* UA,UG,C,A,C */ + -310 80 -310 -360 /* UA,UG,C,A,G */ + 30 180 30 -260 /* UA,UG,C,A,U */ + 30 180 30 -260 /* UA,UG,C,C,A */ + 30 180 30 -260 /* UA,UG,C,C,C */ + 30 180 30 -260 /* UA,UG,C,C,G */ + 30 180 30 -260 /* UA,UG,C,C,U */ + -480 -90 -480 -530 /* UA,UG,C,G,A */ + 30 180 30 -260 /* UA,UG,C,G,C */ + 1280 1430 1280 990 /* UA,UG,C,G,G */ + 30 180 30 -260 /* UA,UG,C,G,U */ + 30 180 30 -260 /* UA,UG,C,U,A */ + 30 180 30 -260 /* UA,UG,C,U,C */ + 30 180 30 -260 /* UA,UG,C,U,G */ + 30 180 30 -260 /* UA,UG,C,U,U */ + -580 690 1470 690 /* UA,UG,G,A,A */ + -1090 180 960 180 /* UA,UG,G,A,C */ + -1430 -160 -630 -160 /* UA,UG,G,A,G */ + -1090 180 960 180 /* UA,UG,G,A,U */ + -1090 180 960 180 /* UA,UG,G,C,A */ + -850 180 960 180 /* UA,UG,G,C,C */ + -1090 180 960 180 /* UA,UG,G,C,G */ + -850 180 960 180 /* UA,UG,G,C,U */ + -1600 -330 -800 -330 /* UA,UG,G,G,A */ + -1090 180 960 180 /* UA,UG,G,G,C */ + -1090 1430 -290 1430 /* UA,UG,G,G,G */ + -1090 180 960 180 /* UA,UG,G,G,U */ + -1090 180 960 180 /* UA,UG,G,U,A */ + -850 180 960 180 /* UA,UG,G,U,C */ + -1090 180 960 180 /* UA,UG,G,U,G */ + -1090 180 -290 180 /* UA,UG,G,U,U */ + 540 560 540 -10 /* UA,UG,U,A,A */ + 30 50 30 -760 /* UA,UG,U,A,C */ + -310 -50 -310 -1100 /* UA,UG,U,A,G */ + 30 50 30 -760 /* UA,UG,U,A,U */ + 30 50 30 -760 /* UA,UG,U,C,A */ + 30 50 30 -760 /* UA,UG,U,C,C */ + 30 50 30 -760 /* UA,UG,U,C,G */ + 30 50 30 -760 /* UA,UG,U,C,U */ + -480 -220 -480 -1270 /* UA,UG,U,G,A */ + 30 50 30 -760 /* UA,UG,U,G,C */ + 1280 1300 1280 -760 /* UA,UG,U,G,G */ + 30 50 30 -760 /* UA,UG,U,G,U */ + 30 50 30 -760 /* UA,UG,U,U,A */ + 30 50 30 -760 /* UA,UG,U,U,C */ + 30 50 30 -760 /* UA,UG,U,U,G */ + 30 50 30 -760 /* UA,UG,U,U,U */ + 1400 1270 -300 1270 /* UA,AU,A,A,A */ + 1090 960 -610 960 /* UA,AU,A,A,C */ + 10 -110 -1690 -110 /* UA,AU,A,A,G */ + 1090 960 -610 960 /* UA,AU,A,A,U */ + 1110 980 -590 980 /* UA,AU,A,C,A */ + 1100 970 -360 970 /* UA,AU,A,C,C */ + 1110 980 -590 980 /* UA,AU,A,C,G */ + 1100 970 -360 970 /* UA,AU,A,C,U */ + 190 60 -1510 60 /* UA,AU,A,G,A */ + 1090 960 -610 960 /* UA,AU,A,G,C */ + 1930 1800 -1020 1800 /* UA,AU,A,G,G */ + 1090 960 -610 960 /* UA,AU,A,G,U */ + 1110 980 -590 980 /* UA,AU,A,U,A */ + 1100 970 -360 970 /* UA,AU,A,U,C */ + 1110 980 -590 980 /* UA,AU,A,U,G */ + 360 0 -1580 0 /* UA,AU,A,U,U */ + 1120 1270 1120 830 /* UA,AU,C,A,A */ + 810 960 810 520 /* UA,AU,C,A,C */ + -260 130 -260 -310 /* UA,AU,C,A,G */ + 810 960 810 520 /* UA,AU,C,A,U */ + 830 980 830 540 /* UA,AU,C,C,A */ + 820 970 820 530 /* UA,AU,C,C,C */ + 830 980 830 540 /* UA,AU,C,C,G */ + 820 970 820 530 /* UA,AU,C,C,U */ + -80 300 -80 -130 /* UA,AU,C,G,A */ + 810 960 810 520 /* UA,AU,C,G,C */ + 1650 1800 1650 1360 /* UA,AU,C,G,G */ + 810 960 810 520 /* UA,AU,C,G,U */ + 830 980 830 540 /* UA,AU,C,U,A */ + 820 970 820 530 /* UA,AU,C,U,C */ + 830 980 830 540 /* UA,AU,C,U,G */ + -150 0 -150 -440 /* UA,AU,C,U,U */ + 0 1270 2050 1270 /* UA,AU,G,A,A */ + -310 960 1740 960 /* UA,AU,G,A,C */ + -1390 -110 -580 -110 /* UA,AU,G,A,G */ + -310 960 1740 960 /* UA,AU,G,A,U */ + -290 980 1760 980 /* UA,AU,G,C,A */ + -60 970 1750 970 /* UA,AU,G,C,C */ + -290 980 1760 980 /* UA,AU,G,C,G */ + -60 970 1750 970 /* UA,AU,G,C,U */ + -1210 60 -400 60 /* UA,AU,G,G,A */ + -310 960 1740 960 /* UA,AU,G,G,C */ + -720 1800 80 1800 /* UA,AU,G,G,G */ + -310 960 1740 960 /* UA,AU,G,G,U */ + -290 980 1760 980 /* UA,AU,G,U,A */ + -60 970 1750 970 /* UA,AU,G,U,C */ + -290 980 1760 980 /* UA,AU,G,U,G */ + -1280 0 -470 0 /* UA,AU,G,U,U */ + 1120 1140 1120 570 /* UA,AU,U,A,A */ + 810 830 810 20 /* UA,AU,U,A,C */ + -260 0 -260 -1050 /* UA,AU,U,A,G */ + 810 830 810 20 /* UA,AU,U,A,U */ + 830 850 830 40 /* UA,AU,U,C,A */ + 820 840 820 30 /* UA,AU,U,C,C */ + 830 850 830 40 /* UA,AU,U,C,G */ + 820 840 820 30 /* UA,AU,U,C,U */ + -80 180 -80 -870 /* UA,AU,U,G,A */ + 810 830 810 20 /* UA,AU,U,G,C */ + 1650 1670 1650 -380 /* UA,AU,U,G,G */ + 810 830 810 20 /* UA,AU,U,G,U */ + 830 850 830 40 /* UA,AU,U,U,A */ + 820 840 820 30 /* UA,AU,U,U,C */ + 830 850 830 40 /* UA,AU,U,U,G */ + -150 -130 -150 -940 /* UA,AU,U,U,U */ + 1470 1340 -230 1340 /* UA,UA,A,A,A */ + 1190 1060 -510 1060 /* UA,UA,A,A,C */ + 60 -60 -1640 -60 /* UA,UA,A,A,G */ + 1190 1060 -510 1060 /* UA,UA,A,A,U */ + 1340 1210 -360 1210 /* UA,UA,A,C,A */ + 1340 1210 -120 1210 /* UA,UA,A,C,C */ + 1340 1210 -360 1210 /* UA,UA,A,C,G */ + 1210 1080 -250 1080 /* UA,UA,A,C,U */ + -230 -360 -1940 -360 /* UA,UA,A,G,A */ + 1190 1060 -510 1060 /* UA,UA,A,G,C */ + 2120 1990 -830 1990 /* UA,UA,A,G,G */ + 1190 1060 -510 1060 /* UA,UA,A,G,U */ + 1340 1210 -360 1210 /* UA,UA,A,U,A */ + 900 770 -560 770 /* UA,UA,A,U,C */ + 1340 1210 -360 1210 /* UA,UA,A,U,G */ + 640 270 -1300 270 /* UA,UA,A,U,U */ + 1190 1340 1190 900 /* UA,UA,C,A,A */ + 910 1060 910 620 /* UA,UA,C,A,C */ + -210 180 -210 -260 /* UA,UA,C,A,G */ + 910 1060 910 620 /* UA,UA,C,A,U */ + 1060 1210 1060 770 /* UA,UA,C,C,A */ + 1060 1210 1060 770 /* UA,UA,C,C,C */ + 1060 1210 1060 770 /* UA,UA,C,C,G */ + 930 1080 930 640 /* UA,UA,C,C,U */ + -510 -120 -510 -560 /* UA,UA,C,G,A */ + 910 1060 910 620 /* UA,UA,C,G,C */ + 1840 1990 1840 1550 /* UA,UA,C,G,G */ + 910 1060 910 620 /* UA,UA,C,G,U */ + 1060 1210 1060 770 /* UA,UA,C,U,A */ + 620 770 620 330 /* UA,UA,C,U,C */ + 1060 1210 1060 770 /* UA,UA,C,U,G */ + 120 270 120 -170 /* UA,UA,C,U,U */ + 60 1340 2120 1340 /* UA,UA,G,A,A */ + -210 1060 1840 1060 /* UA,UA,G,A,C */ + -1340 -60 -530 -60 /* UA,UA,G,A,G */ + -210 1060 1840 1060 /* UA,UA,G,A,U */ + -60 1210 1990 1210 /* UA,UA,G,C,A */ + 180 1210 1990 1210 /* UA,UA,G,C,C */ + -60 1210 1990 1210 /* UA,UA,G,C,G */ + 50 1080 1860 1080 /* UA,UA,G,C,U */ + -1640 -360 -830 -360 /* UA,UA,G,G,A */ + -210 1060 1840 1060 /* UA,UA,G,G,C */ + -530 1990 270 1990 /* UA,UA,G,G,G */ + -210 1060 1840 1060 /* UA,UA,G,G,U */ + -60 1210 1990 1210 /* UA,UA,G,U,A */ + -260 770 1550 770 /* UA,UA,G,U,C */ + -60 1210 1990 1210 /* UA,UA,G,U,G */ + -1000 270 -200 270 /* UA,UA,G,U,U */ + 1190 1210 1190 640 /* UA,UA,U,A,A */ + 910 930 910 120 /* UA,UA,U,A,C */ + -210 50 -210 -1000 /* UA,UA,U,A,G */ + 910 930 910 120 /* UA,UA,U,A,U */ + 1060 1080 1060 270 /* UA,UA,U,C,A */ + 1060 1080 1060 270 /* UA,UA,U,C,C */ + 1060 1080 1060 270 /* UA,UA,U,C,G */ + 930 950 930 140 /* UA,UA,U,C,U */ + -510 -250 -510 -1300 /* UA,UA,U,G,A */ + 910 930 910 120 /* UA,UA,U,G,C */ + 1840 1860 1840 -200 /* UA,UA,U,G,G */ + 910 930 910 120 /* UA,UA,U,G,U */ + 1060 1080 1060 270 /* UA,UA,U,U,A */ + 620 640 620 -170 /* UA,UA,U,U,C */ + 1060 1080 1060 270 /* UA,UA,U,U,G */ + 120 140 120 -670 /* UA,UA,U,U,U */ + +# hairpin + INF INF INF 540 560 570 540 600 550 640 + 650 660 670 680 690 690 700 710 710 720 + 720 730 730 740 740 750 750 750 760 760 + 770 + +# hairpin_enthalpies + INF INF INF 130 480 360 -290 130 -290 500 + 500 500 500 500 500 500 500 500 500 500 + 500 500 500 500 500 500 500 500 500 500 + 500 + +# bulge + INF 380 280 320 360 400 440 460 470 480 + 490 500 510 520 530 540 540 550 550 560 + 570 570 580 580 580 590 590 600 600 600 + 610 + +# bulge_enthalpies + INF 1060 710 710 710 710 710 710 710 710 + 710 710 710 710 710 710 710 710 710 710 + 710 710 710 710 710 710 710 710 710 710 + 710 + +# interior + INF INF 100 100 110 200 200 210 230 240 + 250 260 270 280 290 290 300 310 310 320 + 330 330 340 340 350 350 350 360 360 370 + 370 + +# interior_enthalpies + INF INF -720 -720 -720 -680 -130 -130 -130 -130 + -130 -130 -130 -130 -130 -130 -130 -130 -130 -130 + -130 -130 -130 -130 -130 -130 -130 -130 -130 -130 + -130 + +# ML_params + 0 0 930 3000 -90 -220 + +# NINIO + 60 320 300 + +# Misc + 410 360 50 370 + +# Hexaloops +ACAGUACU 280 -1680 +ACAGUGAU 360 -1140 +ACAGUGCU 290 -1280 +ACAGUGUU 180 -1540 + +# Tetraloops +CAACGG 550 690 +CCAAGG 330 -1030 +CCACGG 370 -330 +CCCAGG 340 -890 +CCGAGG 350 -660 +CCGCGG 360 -750 +CCUAGG 370 -350 +CCUCGG 250 -1390 +CUAAGG 360 -760 +CUACGG 280 -1070 +CUCAGG 370 -660 +CUCCGG 270 -1290 +CUGCGG 280 -1070 +CUUAGG 350 -620 +CUUCGG 370 -1530 +CUUUGG 370 -680 + +# Triloops +CAACG 680 2370 +GUUAC 690 1080 + + + +#END diff --git a/src/evd.cpp b/src/evd.cpp new file mode 100644 index 0000000..643295a --- /dev/null +++ b/src/evd.cpp @@ -0,0 +1,210 @@ +#include "evd.h" + +EVD::EVD(vector dist, int C) { + lambda=mu=sum_of_elements=num_iterations=0; + data=dist; + size = data.size(); + for(vector::iterator it = data.begin(); it != data.end(); ++it) + sum_of_elements += *it; + CENSORED = C; +} + +EVD::~EVD() { + +} + +void EVD::printHistogram(double min, double max, double bin_size){ + int total = 0,relative; + for(int i=0; i::iterator it=data.begin();it!=data.end();++it){ + if(max<*it){ + max=*it;} + if(min>*it){ + min=*it;} + } + bin_size = (max - min)/NUM_BINS; + for(vector::iterator it=data.begin();it!=data.end();++it){ + if(fabs(*it-max) <0.0001) + bin_index = NUM_BINS-1; + else + bin_index = floor(fabs(*it-min)/bin_size); + histogram[bin_index].push_back(*it); + } + printHistogram(min,max,bin_size); + return; +} + +double EVD::pvalue(double x, double mu, double lambda){ + return exp(-exp(-lambda*(x-mu))); +} + +int EVD::totalFit(vector data){ + int i; + int max_it_num=100; + double thresh = 0.00001; + double lam,x,expsum,xexpsum,x2expsum,e,f,fprime; + int n =data.size(); + //Initialize lambda + lam = 0.2; + + //update lambda until convergence or many iterations + for(num_iterations=0;num_iterations data, double c, int z){ + int i; + int max_it_num=100; + double thresh = 0.00001; + double lam,x,expsum,xexpsum,x2expsum,e,f,fprime; + double psx; + double explamc ; + + //Initialize lambda + lam = 0.2; + + + //update lambda until convergence or many iterations + for(num_iterations=0;num_iterations censored_data, new_censored_data; + int prev_count=0; + double prev_mu=-99999,prev_lam=-99999; + const float TH= 0.0001; + + //printf("new highbound:%f,new lowbound:%f\n",highbound,lowbound); + censored_data = data; + totalFit(censored_data); + //printf("mu=%f,lambda=%f,\n",mu,lambda); + //printf("*************\n"); + + for(num_iterations=1;num_iterations<=max_it_num;num_iterations++){ + new_censored_data.clear(); + //construct the censored vector + lowbound = (double) (1./(censored_data.size()+1.)); + highbound = (double) (censored_data.size()/(censored_data.size()+1.)); + //printf("******CENSORED******\niteration=%d\n",num_iterations); + //printf("mu=%f,lambda=%f,\n",mu,lambda); + //printf("new highbound:%f,new lowbound:%f\n",highbound,lowbound); + //printf("data_size:%d\n",censored_data.size()); + for(i=0;i= lowbound) + new_censored_data.push_back(censored_data[i]); + } + //printf("new_data_size:%d\n",new_censored_data.size()); + + + if((new_censored_data.size()-censored_data.size())==0 || (fabs(lambda-prev_lam) +#include +#include +#include +#include + +using namespace std; + +class EVD { +public: + EVD(vector, int C); + virtual ~EVD(); + double getStats(); + int fit(); + double getLambda(){return lambda;} + double getMu(){return mu;} + int getSize(){return size;} + int getNumIter(){return num_iterations;} + double getSum(){return sum_of_elements;} + + +private: + vector data; + double lambda; + double mu; + int size; + double sum_of_elements; + int num_iterations; + int CENSORED; //Ignore the left tail in fitting + vector< vector > histogram; + void makeHistogram(); + void printHistogram(double min, double max, double bin_size); + int censoredFit(vector data, double c, int z); + int totalFit(vector data); + double pvalue(double x, double mu, double lambda); +}; + +#endif /* EVD_H_ */ diff --git a/src/fold.h b/src/fold.h new file mode 100644 index 0000000..f12b201 --- /dev/null +++ b/src/fold.h @@ -0,0 +1,604 @@ +#ifndef __VIENNA_RNA_PACKAGE_FOLD_H__ +#define __VIENNA_RNA_PACKAGE_FOLD_H__ + +#include "data_structures.h" + +#ifdef __GNUC__ +#define DEPRECATED(func) func __attribute__ ((deprecated)) +#else +#define DEPRECATED(func) func +#endif + +/** + * \addtogroup mfe_fold + * \ingroup folding_routines + * \brief This section covers all functions and variables related to the calculation + * of minimum free energy (MFE) structures. + * + * The library provides a fast dynamic programming minimum free energy + * folding algorithm as described in \cite zuker:1981. + * All relevant parts that directly implement the "Zuker & Stiegler" algorithm for single + * sequences are described in this section. + * + * Folding of circular RNA sequences is handled as a post-processing step of the forward + * recursions. See \cite hofacker:2006 for further details. + * + * Nevertheless, the RNAlib also + * provides interfaces for the prediction of consensus MFE structures of sequence alignments, + * MFE structure for two hybridized sequences, local optimal structures and many more. For + * those more specialized variants of MFE folding routines, please consult the appropriate + * subsections (Modules) as listed above. + * + * \file fold.h + * \brief MFE calculations and energy evaluations for single RNA sequences + * + * This file includes (almost) all function declarations within the RNAlib that are related to + * MFE folding... + */ + +/** + * \defgroup eval Energy evaluation + * @{ + * \brief This module contains all functions and variables related to energy evaluation + * of sequence/structure pairs. + * + * + * @} + */ + +/** + * \defgroup mfe_fold Calculating Minimum Free Energy Structures + * @{ + * \brief This module contains all functions and variables related to the calculation + * of global minimum free energy structures for single sequences. + * + * The library provides a fast dynamic programming minimum free energy + * folding algorithm as described by \ref zuker_81 "Zuker & Stiegler (1981)". + * @} + */ + +/** \brief if nonzero use logarithmic ML energy in energy_of_struct */ +extern int logML; + +/** \brief do ML decomposition uniquely (for subopt) */ +extern int uniq_ML; + +/** \brief set to first pos of second seq for cofolding */ +extern int cut_point; + +/** + * \brief verbose info from energy_of_struct + * \ingroup eval + */ +extern int eos_debug; + + +/** + * \brief Compute minimum free energy and an appropriate secondary + * structure of an RNA sequence + * + * The first parameter given, the RNA sequence, must be \a uppercase and should only contain + * an alphabet \f$\Sigma\f$ that is understood by the RNAlib\n + * (e.g. \f$ \Sigma = \{A,U,C,G\} \f$)\n + * + * The second parameter, \a structure, must always point to an allocated + * block of memory with a size of at least \f$\mathrm{strlen}(\mathrm{sequence})+1\f$ + * + * If the third parameter is NULL, global model detail settings are assumed for the folding + * recursions. Otherwise, the provided parameters are used. + * + * The fourth parameter indicates whether a secondary structure constraint in enhanced dot-bracket + * notation is passed through the structure parameter or not. If so, the characters " | x < > " are + * recognized to mark bases that are paired, unpaired, paired upstream, or downstream, respectively. + * Matching brackets " ( ) " denote base pairs, dots "." are used for unconstrained bases. + * + * To indicate that the RNA sequence is circular and thus has to be post-processed, set the last + * parameter to non-zero + * + * After a successful call of fold_par(), a backtracked secondary structure (in dot-bracket notation) + * that exhibits the minimum of free energy will be written to the memory \a structure is pointing to. + * The function returns the minimum of free energy for any fold of the sequence given. + * + * \note OpenMP: Passing NULL to the 'parameters' argument involves access to several global model + * detail variables and thus is not to be considered threadsafe + * + * \ingroup mfe_fold + * + * \see fold(), circfold(), #model_detailsT, set_energy_model(), get_scaled_parameters() + * + * \param sequence RNA sequence + * \param structure A pointer to the character array where the + * secondary structure in dot-bracket notation will be written to + * \param parameters A data structure containing the prescaled energy contributions + * and the model details. (NULL may be passed, see OpenMP notes above) + * \param is_constrained Switch to indicate that a structure contraint is passed via the structure argument (0==off) + * \param is_circular Switch to (de-)activate postprocessing steps in case RNA sequence is circular (0==off) + * + * \return the minimum free energy (MFE) in kcal/mol + */ +float fold_par( const char *sequence, + char *structure, + paramT *parameters, + int is_constrained, + int is_circular); + +/** + * \brief Compute minimum free energy and an appropriate secondary structure of an RNA sequence + * + * This function essentially does the same thing as fold_par(). However, it takes its model details, + * i.e. #temperature, #dangles, #tetra_loop, #noGU, #no_closingGU, #fold_constrained, #noLonelyPairs + * from the current global settings within the library + * + * Use fold_par() for a completely threadsafe variant + * + * \ingroup mfe_fold + * + * \see fold_par(), circfold() + * + * \param sequence RNA sequence + * \param structure A pointer to the character array where the + * secondary structure in dot-bracket notation will be written to + * \return the minimum free energy (MFE) in kcal/mol + */ +float fold( const char *sequence, + char *structure); + +/** + * \brief Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence + * + * This function essentially does the same thing as fold_par(). However, it takes its model details, + * i.e. #temperature, #dangles, #tetra_loop, #noGU, #no_closingGU, #fold_constrained, #noLonelyPairs + * from the current global settings within the library + * + * Use fold_par() for a completely threadsafe variant + * + * \ingroup mfe_fold + * + * \see fold_par(), circfold() + * + * \param sequence RNA sequence + * \param structure A pointer to the character array where the + * secondary structure in dot-bracket notation will be written to + * \return the minimum free energy (MFE) in kcal/mol + */ +float circfold( const char *sequence, + char *structure); + + +/** + * \addtogroup eval Energy evaluation + * \ingroup folding_routines + * @{ + * \brief This module contains all functions and variables related to energy evaluation + * of sequence/structure pairs. + * @} + */ + +/** + * \brief Calculate the free energy of an already folded RNA using global model detail settings + * + * If verbosity level is set to a value >0, energies of structure elements are printed to stdout + * + * \note OpenMP: This function relies on several global model settings variables and thus is + * not to be considered threadsafe. See energy_of_struct_par() for a completely threadsafe + * implementation. + * + * \ingroup eval + * + * \see energy_of_struct_par(), energy_of_circ_structure() + * + * \param string RNA sequence + * \param structure secondary structure in dot-bracket notation + * \param verbosity_level a flag to turn verbose output on/off + * \return the free energy of the input structure given the input sequence in kcal/mol + */ +float energy_of_structure(const char *string, + const char *structure, + int verbosity_level); + +/** + * \brief Calculate the free energy of an already folded RNA + * + * If verbosity level is set to a value >0, energies of structure elements are printed to stdout + * + * \ingroup eval + * + * \see energy_of_circ_structure(), energy_of_structure_pt(), get_scaled_parameters() + * + * \param string RNA sequence in uppercase letters + * \param structure Secondary structure in dot-bracket notation + * \param parameters A data structure containing the prescaled energy contributions and the model details. + * \param verbosity_level A flag to turn verbose output on/off + * \return The free energy of the input structure given the input sequence in kcal/mol + */ +float energy_of_struct_par( const char *string, + const char *structure, + paramT *parameters, + int verbosity_level); + +/** + * \brief Calculate the free energy of an already folded circular RNA + * + * \note OpenMP: This function relies on several global model settings variables and thus is + * not to be considered threadsafe. See energy_of_circ_struct_par() for a completely threadsafe + * implementation. + * + * If verbosity level is set to a value >0, energies of structure elements are printed to stdout + * + * \ingroup eval + * + * \see energy_of_circ_struct_par(), energy_of_struct_par() + * + * \param string RNA sequence + * \param structure Secondary structure in dot-bracket notation + * \param verbosity_level A flag to turn verbose output on/off + * \return The free energy of the input structure given the input sequence in kcal/mol + */ +float energy_of_circ_structure( const char *string, + const char *structure, + int verbosity_level); + +/** + * \brief Calculate the free energy of an already folded circular RNA + * + * If verbosity level is set to a value >0, energies of structure elements are printed to stdout + * + * \ingroup eval + * + * \see energy_of_struct_par(), get_scaled_parameters() + * + * \param string RNA sequence + * \param structure Secondary structure in dot-bracket notation + * \param parameters A data structure containing the prescaled energy contributions and the model details. + * \param verbosity_level A flag to turn verbose output on/off + * \return The free energy of the input structure given the input sequence in kcal/mol + */ +float energy_of_circ_struct_par(const char *string, + const char *structure, + paramT *parameters, + int verbosity_level); + + +float energy_of_gquad_structure(const char *string, + const char *structure, + int verbosity_level); + +float energy_of_gquad_struct_par( const char *string, + const char *structure, + paramT *parameters, + int verbosity_level); + +/** + * \brief Calculate the free energy of an already folded RNA + * + * If verbosity level is set to a value >0, energies of structure elements are printed to stdout + * + * \note OpenMP: This function relies on several global model settings variables and thus is + * not to be considered threadsafe. See energy_of_struct_pt_par() for a completely threadsafe + * implementation. + * + * \ingroup eval + * + * \see make_pair_table(), energy_of_struct_pt_par() + * + * \param string RNA sequence + * \param ptable the pair table of the secondary structure + * \param s encoded RNA sequence + * \param s1 encoded RNA sequence + * \param verbosity_level a flag to turn verbose output on/off + * \return the free energy of the input structure given the input sequence in 10kcal/mol + */ +int energy_of_structure_pt( const char *string, + short *ptable, + short *s, + short *s1, + int verbosity_level); + +/** + * \brief Calculate the free energy of an already folded RNA + * + * If verbosity level is set to a value >0, energies of structure elements are printed to stdout + * + * \ingroup eval + * + * \see make_pair_table(), energy_of_struct_par(), get_scaled_parameters() + * + * \param string RNA sequence in uppercase letters + * \param ptable The pair table of the secondary structure + * \param s Encoded RNA sequence + * \param s1 Encoded RNA sequence + * \param parameters A data structure containing the prescaled energy contributions and the model details. + * \param verbosity_level A flag to turn verbose output on/off + * \return The free energy of the input structure given the input sequence in 10kcal/mol + */ +int energy_of_struct_pt_par(const char *string, + short *ptable, + short *s, + short *s1, + paramT *parameters, + int verbosity_level); + +/** + * \brief Free arrays for mfe folding + * + * \ingroup mfe_fold + * + */ +void free_arrays(void); + + +/** + * \brief Create a dot-backet/parenthesis structure from backtracking stack + * + * \note This function is threadsafe + */ +void parenthesis_structure(char *structure, + bondT *bp, + int length); + +/** + * \brief Create a dot-backet/parenthesis structure from backtracking stack + * obtained by zuker suboptimal calculation in cofold.c + * + * \note This function is threadsafe + */ +void parenthesis_zuker( char *structure, + bondT *bp, + int length); + +void letter_structure(char *structure, + bondT *bp, + int length); + + +/** + * \brief Recalculate energy parameters + * + * \ingroup mfe_fold + */ +void update_fold_params(void); + +/** + * + * \ingroup mfe_fold + * + */ +void update_fold_params_par(paramT *parameters); + +/** + * + * \ingroup mfe_fold + * + */ +char *backtrack_fold_from_pair(char *sequence, + int i, + int j); + +/** + * \brief Calculate energy of a move (closing or opening of a base pair) + * + * If the parameters m1 and m2 are negative, it is deletion (opening) + * of a base pair, otherwise it is insertion (opening). + * + * \see make_pair_table(), energy_of_move() + * \param string RNA sequence + * \param structure secondary structure in dot-bracket notation + * \param m1 first coordinate of base pair + * \param m2 second coordinate of base pair + * \returns energy change of the move in kcal/mol + */ +float energy_of_move( const char *string, + const char *structure, + int m1, + int m2); + + +/** + * + * \brief Calculate energy of a move (closing or opening of a base pair) + * + * If the parameters m1 and m2 are negative, it is deletion (opening) + * of a base pair, otherwise it is insertion (opening). + * + * \see make_pair_table(), energy_of_move() + * \param pt the pair table of the secondary structure + * \param s encoded RNA sequence + * \param s1 encoded RNA sequence + * \param m1 first coordinate of base pair + * \param m2 second coordinate of base pair + * \returns energy change of the move in 10cal/mol + */ +int energy_of_move_pt(short *pt, + short *s, + short *s1, + int m1, + int m2); + +/** + * \brief Calculate energy of a loop + * + * \param ptable the pair table of the secondary structure + * \param s encoded RNA sequence + * \param s1 encoded RNA sequence + * \param i position of covering base pair + * \returns free energy of the loop in 10cal/mol + */ +int loop_energy(short *ptable, + short *s, + short *s1, + int i); + +/** + * + * \ingroup mfe_fold + * + */ +void export_fold_arrays(int **f5_p, + int **c_p, + int **fML_p, + int **fM1_p, + int **indx_p, + char **ptype_p); + +/** + * + * \ingroup mfe_fold + * + */ +void export_fold_arrays_par(int **f5_p, + int **c_p, + int **fML_p, + int **fM1_p, + int **indx_p, + char **ptype_p, + paramT **P_p); + +/** + * + * \ingroup mfe_fold + * + */ +void export_circfold_arrays(int *Fc_p, + int *FcH_p, + int *FcI_p, + int *FcM_p, + int **fM2_p, + int **f5_p, + int **c_p, + int **fML_p, + int **fM1_p, + int **indx_p, + char **ptype_p); + +/** + * + * \ingroup mfe_fold + * + */ +void export_circfold_arrays_par(int *Fc_p, + int *FcH_p, + int *FcI_p, + int *FcM_p, + int **fM2_p, + int **f5_p, + int **c_p, + int **fML_p, + int **fM1_p, + int **indx_p, + char **ptype_p, + paramT **P_p); + + +/** + * \brief Create a plist from a dot-bracket string + * + * The dot-bracket string is parsed and for each base pair an + * entry in the plist is created. The probability of each pair in + * the list is set by a function parameter. + * + * The end of the plist is marked by sequence positions i as well as j + * equal to 0. This condition should be used to stop looping over its + * entries + * + * This function is threadsafe + * + * \param pl A pointer to the plist that is to be created + * \param struc The secondary structure in dot-bracket notation + * \param pr The probability for each base pair + */ +void assign_plist_from_db(plist **pl, + const char *struc, + float pr); + +/* finally moved the loop energy function declarations to this header... */ +/* BUT: The functions only exist for backward compatibility reasons! */ +/* You better include "loop_energies.h" and call the functions: */ +/* E_Hairpin() and E_IntLoop() which are (almost) threadsafe as they get */ +/* a pointer to the energy parameter datastructure as additional argument */ + +/** + * \deprecated {This function is deprecated and will be removed soon. + * Use \ref E_IntLoop() instead!} + */ +DEPRECATED(int LoopEnergy(int n1, + int n2, + int type, + int type_2, + int si1, + int sj1, + int sp1, + int sq1)); + +/** + * \deprecated {This function is deprecated and will be removed soon. + * Use \ref E_Hairpin() instead!} + */ +DEPRECATED(int HairpinE(int size, + int type, + int si1, + int sj1, + const char *string)); + +/** + * Allocate arrays for folding\n + * \deprecated {This function is deprecated and will be removed soon!} + * + */ +DEPRECATED(void initialize_fold(int length)); + +/** + * Calculate the free energy of an already folded RNA + * + * \note This function is not entirely threadsafe! Depending on the state of the global + * variable \ref eos_debug it prints energy information to stdout or not...\n + * + * \deprecated This function is deprecated and should not be used in future programs! + * Use \ref energy_of_structure() instead! + * + * \see energy_of_structure, energy_of_circ_struct(), energy_of_struct_pt() + * \param string RNA sequence + * \param structure secondary structure in dot-bracket notation + * \return the free energy of the input structure given the input sequence in kcal/mol + */ +DEPRECATED(float energy_of_struct(const char *string, + const char *structure)); + +/** + * Calculate the free energy of an already folded RNA + * + * \note This function is not entirely threadsafe! Depending on the state of the global + * variable \ref eos_debug it prints energy information to stdout or not...\n + * + * \deprecated This function is deprecated and should not be used in future programs! + * Use \ref energy_of_structure_pt() instead! + * + * \see make_pair_table(), energy_of_structure() + * \param string RNA sequence + * \param ptable the pair table of the secondary structure + * \param s encoded RNA sequence + * \param s1 encoded RNA sequence + * \return the free energy of the input structure given the input sequence in 10kcal/mol + */ +DEPRECATED(int energy_of_struct_pt( const char *string, + short *ptable, + short *s, + short *s1)); + +/** + * Calculate the free energy of an already folded circular RNA + * + * \note This function is not entirely threadsafe! Depending on the state of the global + * variable \ref eos_debug it prints energy information to stdout or not...\n + * + * \deprecated This function is deprecated and should not be used in future programs + * Use \ref energy_of_circ_structure() instead! + * + * \see energy_of_circ_structure(), energy_of_struct(), energy_of_struct_pt() + * \param string RNA sequence + * \param structure secondary structure in dot-bracket notation + * \return the free energy of the input structure given the input sequence in kcal/mol + */ +DEPRECATED(float energy_of_circ_struct( const char *string, + const char *structure)); + +#endif diff --git a/src/fold_vars.h b/src/fold_vars.h new file mode 100644 index 0000000..3ebf8ec --- /dev/null +++ b/src/fold_vars.h @@ -0,0 +1,221 @@ +#ifndef __VIENNA_RNA_PACKAGE_FOLD_VARS_H__ +#define __VIENNA_RNA_PACKAGE_FOLD_VARS_H__ + +#include "data_structures.h" + +/** + * \file fold_vars.h + * \brief Here all all declarations of the global variables used throughout RNAlib + */ + + +#define PUBLIC +#define PRIVATE static + +/** + * \brief Global switch to activate/deactivate folding with structure constraints + */ +extern int fold_constrained; + +/** + * \brief Global switch to avoid/allow helices of length 1 + * + * Disallow all pairs which can only occur as lonely pairs (i.e. as helix + * of length 1). This avoids lonely base pairs in the predicted structures in + * most cases. + */ +extern int noLonelyPairs; + +/** + * \brief Switch the energy model for dangling end contributions (0, 1, 2, 3) + * + * If set to 0 no stabilizing energies are assigned to bases adjacent to + * helices in free ends and multiloops (so called dangling ends). Normally + * (dangles = 1) dangling end energies are assigned only to unpaired + * bases and a base cannot participate simultaneously in two dangling ends. In + * the partition function algorithm pf_fold() these checks are neglected. + * If #dangles is set to 2, all folding routines will follow this convention. + * This treatment of dangling ends gives more favorable energies to helices + * directly adjacent to one another, which can be beneficial since such + * helices often do engage in stabilizing interactions through co-axial + * stacking.\n + * If dangles = 3 co-axial stacking is explicitly included for + * adjacent helices in mutli-loops. The option affects only mfe folding + * and energy evaluation (fold() and energy_of_structure()), as + * well as suboptimal folding (subopt()) via re-evaluation of energies. + * Co-axial stacking with one intervening mismatch is not considered so far. + * + * Default is 2 in most algorithms, partition function algorithms can only handle 0 and 2 + */ +extern int dangles; + +/** + * \brief Global switch to forbid/allow GU base pairs at all + */ +extern int noGU; + +/** + * \brief GU allowed only inside stacks if set to 1 + */ +extern int no_closingGU; + +/** + * \brief Include special stabilizing energies for some tri-, tetra- and hexa-loops; + * + * default is 1. + */ +extern int tetra_loop; + +/** + * \brief 0 = BP; 1=any mit GC; 2=any mit AU-parameter + * + * If set to 1 or 2: fold sequences from an artificial alphabet ABCD..., where A + * pairs B, C pairs D, etc. using either GC (1) or AU parameters (2); + * default is 0, you probably don't want to change it. + */ +extern int energy_set; + +/** + * \brief backward compatibility variable.. this does not effect anything + */ +extern int circ; + +/** + * \brief generate comma seperated output + */ +extern int csv; + +/** + * use old alifold energies (with gaps) + */ +extern int oldAliEn; +/** + * use ribosum matrices + */ +extern int ribo; + +/** + * warning this variable will vanish in the future + * ribosums will be compiled in instead + */ +extern char *RibosumFile; + +/** + * \brief contains allowed non standard base pairs + * + * Lists additional base pairs that will be allowed to form in addition to + * GC, CG, AU, UA, GU and UG. Nonstandard base pairs are given a stacking + * energy of 0. + */ +extern char *nonstandards; + +/** + * \brief Rescale energy parameters to a temperature in degC. + * + * Default is 37C. You have to call the update_..._params() functions after + * changing this parameter. + */ +extern double temperature; + +/** + * interior loops of size 2 get energy 0.8Kcal and + * no mismatches, default 1 + */ +extern int james_rule; + +/** + * use logarithmic multiloop energy function + */ +extern int logML; + +/** + * \brief Marks the position (starting from 1) of the first + * nucleotide of the second molecule within the concatenated sequence. + * + * To evaluate the energy of a duplex structure (a structure formed by two + * strands), concatenate the to sequences and set it to the + * first base of the second strand in the concatenated sequence. + * The default value of -1 stands for single molecule folding. The + * cut_point variable is also used by PS_rna_plot() and + * PS_dot_plot() to mark the chain break in postscript plots. + */ +extern int cut_point; + +/** + * \brief Contains a list of base pairs after a call to fold(). + * + * base_pair[0].i contains the total number of pairs. + * \deprecated Do not use this variable anymore! + */ +extern bondT *base_pair; + +/** + * \brief A pointer to the base pair probability matrix + * + * \deprecated Do not use this variable anymore! + */ +extern FLT_OR_DBL *pr; + +/** + * \brief index array to move through pr. + * + * The probability for base i and j to form a pair is in pr[iindx[i]-j]. + * \deprecated Do not use this variable anymore! + */ +extern int *iindx; + +/** + * \brief A scaling factor used by pf_fold() to avoid overflows. + * + * Should be set to approximately \f$exp{((-F/kT)/length)}\f$, where \f$F\f$ is an estimate + * for the ensemble free energy, for example the minimum free energy. You must + * call update_pf_params() after changing this parameter.\n + * If pf_scale is -1 (the default) , an estimate will be provided + * automatically when computing partition functions, e.g. pf_fold() + * The automatic estimate is usually insufficient for sequences more + * than a few hundred bases long. + */ +extern double pf_scale; + +/** + * \brief do backtracking, i.e. compute secondary structures or base pair probabilities + * + * If 0, do not calculate pair probabilities in pf_fold(); this is about + * twice as fast. Default is 1. + */ +extern int do_backtrack; + +/** + * \brief A backtrack array marker for inverse_fold() + * + * If set to 'C': force (1,N) to be paired, + * 'M' fold as if the sequence were inside a multi-loop. Otherwise ('F') the + * usual mfe structure is computed. + */ +extern char backtrack_type; + +/** + * \brief Allow G-quadruplex formation + */ +extern int gquad; + +/** + * Do not use this variable, it will eventually be removed in one of the next versions + */ +extern int canonicalBPonly; + +char * option_string(void); + +/** + * \brief Set default model details + * + * Use this function if you wish to initialize a #model_detailsT data structure with + * its default values, i.e. the global model settings + * + * \see + * + * \param md A pointer to the data structure that shall be initialized + */ +void set_model_details(model_detailsT *md); + +#endif diff --git a/src/karlin_altschul.cpp b/src/karlin_altschul.cpp new file mode 100644 index 0000000..160c1da --- /dev/null +++ b/src/karlin_altschul.cpp @@ -0,0 +1,117 @@ +#include "karlin_altschul.h" + +void karlin_altschul(const score_prob &sc_pr, double & K, double &lambda ){ + lambda = computeLambda(sc_pr); + + K = computeK(sc_pr,lambda); + //printf("Lambda=%f\n",lambda); + //printf("K=%f\n",K); +} + +double computeH(const score_prob &sc_pr,double lam){ + double H=0.0; + double sc,pr; + for ( mapit it = sc_pr.scmap.begin(); it != sc_pr.scmap.end(); ++it ){ + sc=it->first;pr=it->second; + H+=sc*pr*exp(sc*lam); + } + return H*lam; +} + +double computeK(const score_prob &sc_pr, double lam){ + //printf("#COMPUTING K...\n"); + //sc_pr.print(); + int MAXIT=50; + double TH=0.001; + int PER=2; + score_prob round_scpr,prev_scpr; + int i,j,m,k; + double numerator=0.0,denom,Cstar; + double sc,pr,prevsc,prevpr; + mapit it,prev; + + if(equal(lam,0)){ + return numeric_limits::quiet_NaN(); + } + + denom=computeH(sc_pr,lam); + //printf("Denome=%f\n",denom); + for ( it = sc_pr.scmap.begin(); it != sc_pr.scmap.end(); ++it ){ + prev_scpr.scmap[round_percision(it->first,PER)] += it->second; + if(it->first<0) + numerator += it->second*exp(it->first*lam); + else + numerator += it->second; + } + for (j=2;jfirst,PER);pr=it->second; + for ( prev = prev_scpr.scmap.begin(); prev != prev_scpr.scmap.end(); ++prev ){ + prevsc=prev->first;prevpr=prev->second; + next_scpr.scmap[round_percision(prevsc + sc,PER)] += prevpr*pr; + } + } + //next_scpr.print(); + //next_scpr.checkProb(); + //printf("exp=%f\n",next_scpr.expectedValue()); + for ( it = next_scpr.scmap.begin(); it != next_scpr.scmap.end(); ++it ){ + sc=it->first;pr=it->second; + if(sc<0) + sum1 += pr*exp(sc*lam); + else + sum2 += pr; + } + numerator+=(sum1+sum2)/j; + //printf("sum1:%f,sum2:%f,numerator:%f\n",sum1,sum2,numerator); + //if(exp(-2.0*numerator)/denom-Cstar < TH){ + //Cstar= exp(-2.0*numerator)/denom; + //break; + //} + if(sum1+sum2 < TH){ + //printf("sum1+sum2=%f,TH=%f\n",sum1+sum2,TH); + Cstar= exp(-2.0*numerator)/denom; + break; + } + Cstar= exp(-2.0*numerator)/denom; + prev_scpr= next_scpr; + } + return Cstar; +} + +double computeLambda(const score_prob &sc_pr){ + double TH=0.00001; + int MAXIT=100; + double sum=0.0,up=0.5,point; + int i; + double sc,pr; + mapit it; + //find an upper bound for lambda + while(sum<=1){ + sum=0.0; + up = 2*up; + for ( it = sc_pr.scmap.begin(); it != sc_pr.scmap.end(); ++it ){ + sc=it->first;pr=it->second; + sum+=pr*exp(up*sc); + } + } + //find lambda using binary search + double low=0.0; + for (i=0;ifirst;pr=it->second; + sum+=pr*exp(point*sc); + } + if((abs(up-low) < TH)) break; + if(sum>1) + up=point; + else + low=point; + //print("up=%f;low=%f;point=%f\n",up,low,point) + } + return low; +} diff --git a/src/karlin_altschul.h b/src/karlin_altschul.h new file mode 100644 index 0000000..b068ed6 --- /dev/null +++ b/src/karlin_altschul.h @@ -0,0 +1,59 @@ +#ifndef KARLIN_ALTSCHUL_H_ +#define KARLIN_ALTSCHUL_H_ +#include +#include +#include +#include +#include "aux.h" + +using namespace std; +typedef map::const_iterator mapit; + +struct score_prob{ + map scmap; + void checkProb(){ + float sum=0.0; + for ( mapit it = scmap.begin(); it != scmap.end(); ++it ){ + sum+=it->second; + } + if (!equal(1,sum)){ + reportErr("Sum of score probabilities is not 1!"); + } + } + double expectedValue(){ + float exp=0.0; + float sc,pr; + for ( mapit it = scmap.begin(); it != scmap.end(); ++it ){ + sc=it->first;pr=it->second; + exp+= sc*pr; + } + return exp; + } + double standard_deviation(double mu){ + float std=0.0; + float sc,pr; + for ( mapit it = scmap.begin(); it != scmap.end(); ++it ){ + sc=it->first;pr=it->second; + std+= pr*(sc-mu)*(sc-mu); + } + return sqrt(std); + } + void print() const{ + float sc,pr; + printf("#SCORE\tPROB\n"); + for ( mapit it = scmap.begin(); it != scmap.end(); ++it ){ + sc=it->first;pr=it->second; + printf("%f\t%f\n",sc,pr); + } + } +}; + + +//#define MAXIT 200; +//#define PER 2;//(PERCISION):round to PER decimal places + +void karlin_altschul(const score_prob &sc_pr, double & K, double &lambda ); +double computeLambda(const score_prob &sc_pr); +double computeK(const score_prob &sc_pr, double lam); +double computeH(const score_prob &sc_pr,double lam); +#endif /* KARLIN_ALTSCHUL_H_ */ diff --git a/src/libRNA.a b/src/libRNA.a new file mode 100644 index 0000000..ad280c3 Binary files /dev/null and b/src/libRNA.a differ diff --git a/src/matrices/RIBOSUM100-25.mat b/src/matrices/RIBOSUM100-25.mat new file mode 100644 index 0000000..a027421 --- /dev/null +++ b/src/matrices/RIBOSUM100-25.mat @@ -0,0 +1,30 @@ +RIBOSUM100-25 + + A C G U +A 1.97 +C -1.34 1.00 +G -0.92 -1.70 0.85 +U -1.01 -0.61 -1.11 1.38 +H: 0.5617 +E: -0.0957 + + AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU +AA -2.60 +AC -8.47 -1.85 +AG -8.82 -9.59 -1.33 +AU -5.08 -1.65 -6.07 4.25 +CA -10.06 -10.55 -10.65 -5.77 -6.21 +CC -13.44 -8.85 -15.14 -2.37 -11.69 -3.46 +CG -3.87 -5.44 -2.57 2.03 -3.24 -5.07 5.22 +CU -12.11 -10.68 -9.36 -4.18 -8.33 -6.86 -4.39 -2.56 +GA -6.63 -7.17 -9.39 -3.79 -7.76 -12.90 -6.03 -7.14 -1.62 +GC -5.22 -2.70 -6.29 2.88 -5.40 -3.75 2.80 -2.20 -2.57 5.49 +GG -9.69 -10.38 -4.22 -4.93 -11.48 -12.06 -4.71 -9.14 -9.91 -4.77 -2.31 +GU -6.50 -4.92 -7.13 0.75 -6.20 -7.10 0.25 -4.41 -6.19 1.42 -5.53 3.32 +UA -2.49 -5.59 -2.82 1.88 -2.91 -6.47 2.93 -4.33 -4.87 1.89 -6.32 0.06 4.72 +UC -12.26 -8.88 -8.01 -4.54 -8.03 -8.95 -4.35 -4.67 -6.98 -4.16 -10.57 -4.61 -3.53 -4.14 +UG -3.55 -7.17 -5.83 -0.39 -6.21 -8.30 1.19 -6.47 -7.67 0.33 -4.34 -1.26 1.04 -4.20 3.19 +UU -8.87 -8.39 -9.76 -2.46 -8.85 -6.64 -3.01 -5.43 -10.15 -3.03 -5.02 -2.58 -1.58 -5.90 -3.64 -0.72 +H: 3.4639 +E: -2.6040 + diff --git a/src/matrices/RIBOSUM100-30.mat b/src/matrices/RIBOSUM100-30.mat new file mode 100644 index 0000000..e69ffa1 --- /dev/null +++ b/src/matrices/RIBOSUM100-30.mat @@ -0,0 +1,30 @@ +RIBOSUM100-30 + + A C G U +A 1.97 +C -1.34 1.00 +G -0.92 -1.70 0.85 +U -1.01 -0.61 -1.11 1.38 +H: 0.5622 +E: -0.0959 + + AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU +AA -2.60 +AC -8.47 -1.85 +AG -8.82 -9.59 -1.33 +AU -5.07 -1.65 -6.07 4.25 +CA -10.06 -10.55 -10.65 -5.78 -6.20 +CC -13.44 -8.85 -15.14 -2.37 -11.69 -3.46 +CG -3.87 -5.44 -2.57 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-1.11 1.38 +H: 0.5628 +E: -0.0961 + + AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU +AA -2.60 +AC -8.47 -1.85 +AG -8.82 -9.59 -1.33 +AU -5.07 -1.65 -6.07 4.25 +CA -10.06 -10.55 -10.65 -5.78 -6.20 +CC -13.45 -8.85 -15.14 -2.37 -11.69 -3.46 +CG -3.87 -5.44 -2.57 2.03 -3.24 -5.07 5.22 +CU -12.10 -10.68 -9.36 -4.18 -8.32 -6.86 -4.39 -2.56 +GA -6.62 -7.17 -9.39 -3.79 -7.76 -12.90 -6.03 -7.14 -1.62 +GC -5.22 -2.70 -6.29 2.88 -5.40 -3.76 2.80 -2.20 -2.57 5.49 +GG -9.69 -10.38 -4.22 -4.93 -11.48 -12.06 -4.71 -9.14 -9.91 -4.78 -2.31 +GU -6.50 -4.92 -7.13 0.75 -6.20 -7.10 0.25 -4.41 -6.19 1.42 -5.53 3.32 +UA -2.49 -5.60 -2.83 1.88 -2.91 -6.47 2.93 -4.33 -4.87 1.89 -6.32 0.06 4.73 +UC -12.26 -8.88 -8.01 -4.54 -8.03 -8.95 -4.35 -4.67 -6.98 -4.16 -10.57 -4.61 -3.53 -4.14 +UG -3.54 -7.17 -5.83 -0.39 -6.21 -8.30 1.19 -6.47 -7.67 0.33 -4.34 -1.26 1.04 -4.20 3.19 +UU -8.87 -8.38 -9.76 -2.45 -8.85 -6.64 -3.01 -5.43 -10.14 -3.03 -5.02 -2.57 -1.58 -5.90 -3.64 -0.71 +H: 3.4641 +E: -2.6042 + diff --git a/src/matrices/RIBOSUM100-40.mat b/src/matrices/RIBOSUM100-40.mat new file mode 100644 index 0000000..47c316e --- /dev/null +++ b/src/matrices/RIBOSUM100-40.mat @@ -0,0 +1,30 @@ +RIBOSUM100-40 + + A C G U +A 1.97 +C -1.35 1.00 +G -0.92 -1.70 0.86 +U -1.01 -0.62 -1.12 1.38 +H: 0.5636 +E: -0.0964 + + AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU +AA -2.60 +AC -8.47 -1.85 +AG -8.82 -9.59 -1.33 +AU -5.07 -1.65 -6.07 4.26 +CA -10.05 -10.55 -10.65 -5.78 -6.20 +CC -13.45 -8.85 -15.14 -2.38 -11.69 -3.46 +CG -3.87 -5.45 -2.57 2.03 -3.24 -5.07 5.22 +CU -12.10 -10.68 -9.36 -4.18 -8.32 -6.86 -4.39 -2.56 +GA -6.62 -7.17 -9.39 -3.79 -7.76 -12.90 -6.03 -7.14 -1.62 +GC -5.23 -2.70 -6.29 2.87 -5.40 -3.76 2.80 -2.20 -2.57 5.49 +GG -9.69 -10.38 -4.22 -4.93 -11.48 -12.07 -4.71 -9.14 -9.91 -4.78 -2.31 +GU -6.50 -4.92 -7.12 0.75 -6.20 -7.10 0.25 -4.41 -6.19 1.42 -5.53 3.32 +UA -2.48 -5.61 -2.82 1.88 -2.91 -6.47 2.93 -4.34 -4.87 1.89 -6.32 0.06 4.73 +UC -12.26 -8.88 -8.01 -4.54 -8.03 -8.95 -4.35 -4.67 -6.98 -4.16 -10.57 -4.61 -3.53 -4.14 +UG -3.54 -7.17 -5.83 -0.39 -6.20 -8.30 1.19 -6.48 -7.67 0.33 -4.34 -1.26 1.04 -4.20 3.19 +UU -8.86 -8.38 -9.76 -2.45 -8.85 -6.64 -3.01 -5.43 -10.14 -3.04 -5.02 -2.57 -1.58 -5.90 -3.65 -0.71 +H: 3.4644 +E: -2.6043 + diff --git a/src/matrices/RIBOSUM100-45.mat b/src/matrices/RIBOSUM100-45.mat new file mode 100644 index 0000000..4285f25 --- /dev/null +++ b/src/matrices/RIBOSUM100-45.mat @@ -0,0 +1,30 @@ +RIBOSUM100-45 + + A C G U +A 1.98 +C -1.35 1.00 +G -0.93 -1.70 0.86 +U -1.02 -0.62 -1.12 1.39 +H: 0.5675 +E: -0.0979 + + AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU +AA -2.59 +AC -8.46 -1.85 +AG -8.81 -9.59 -1.32 +AU -5.09 -1.65 -6.06 4.26 +CA -10.05 -10.54 -10.64 -5.78 -6.20 +CC -13.45 -8.86 -15.13 -2.38 -11.69 -3.46 +CG -3.87 -5.48 -2.58 2.02 -3.24 -5.08 5.22 +CU -12.09 -10.68 -9.35 -4.18 -8.32 -6.86 -4.39 -2.55 +GA -6.61 -7.16 -9.38 -3.78 -7.78 -12.91 -6.03 -7.13 -1.62 +GC -5.23 -2.71 -6.29 2.87 -5.40 -3.76 2.79 -2.21 -2.58 5.48 +GG -9.68 -10.38 -4.22 -4.93 -11.48 -12.08 -4.72 -9.15 -9.99 -4.79 -2.31 +GU -6.52 -4.93 -7.12 0.74 -6.20 -7.11 0.24 -4.41 -6.18 1.42 -5.53 3.32 +UA -2.48 -5.61 -2.82 1.87 -2.91 -6.48 2.92 -4.37 -4.87 1.88 -6.34 0.06 4.73 +UC -12.25 -8.87 -8.01 -4.55 -8.02 -8.94 -4.35 -4.66 -6.97 -4.18 -10.57 -4.61 -3.53 -4.13 +UG -3.55 -7.17 -5.82 -0.40 -6.21 -8.31 1.19 -6.51 -7.67 0.32 -4.34 -1.27 1.05 -4.22 3.19 +UU -8.85 -8.38 -9.78 -2.45 -8.84 -6.63 -3.00 -5.42 -10.15 -3.05 -5.02 -2.57 -1.58 -5.89 -3.66 -0.70 +H: 3.4667 +E: -2.6057 + diff --git a/src/matrices/RIBOSUM100-50.mat b/src/matrices/RIBOSUM100-50.mat new file mode 100644 index 0000000..00c0e79 --- /dev/null +++ b/src/matrices/RIBOSUM100-50.mat @@ -0,0 +1,30 @@ +RIBOSUM100-50 + + A C G U +A 2.13 +C -1.64 1.11 +G -1.23 -2.06 0.96 +U -1.27 -0.83 -1.42 1.55 +H: 0.7412 +E: -0.1747 + + AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU +AA -2.18 +AC -8.10 -1.75 +AG -8.47 -9.49 -0.95 +AU -4.90 -1.87 -5.87 4.46 +CA -9.68 -10.27 -10.70 -5.98 -5.84 +CC -13.59 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b/src/matrices/RIBOSUM95-75.mat new file mode 100644 index 0000000..035edbd --- /dev/null +++ b/src/matrices/RIBOSUM95-75.mat @@ -0,0 +1,30 @@ +RIBOSUM95-75 + + A C G U +A 2.32 +C -2.31 1.32 +G -1.98 -2.84 1.15 +U -1.91 -1.27 -2.21 1.76 +H: 1.0970 +E: -0.3818 + + AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU +AA -1.44 +AC -8.72 -1.42 +AG -8.74 -8.65 -0.60 +AU -4.91 -2.30 -5.76 4.77 +CA -10.10 -9.88 -10.92 -6.46 -4.98 +CC -13.36 -8.63 -14.58 -7.17 -11.02 -2.18 +CG -5.33 -5.66 -4.61 1.16 -3.63 -5.17 5.54 +CU -11.58 -11.12 -8.86 -5.67 -7.62 -6.66 -4.85 -1.42 +GA -6.08 -10.24 -9.77 -6.82 -8.57 -13.25 -6.64 -6.87 -0.87 +GC -4.72 -3.71 -6.29 2.30 -6.23 -3.92 1.52 -6.43 -5.45 5.73 +GG -10.32 -12.50 -5.11 -6.48 -11.71 -11.96 -4.47 -12.87 -9.26 -5.09 -2.05 +GU -6.43 -5.85 -7.03 0.39 -8.39 -8.01 -0.95 -6.68 -6.50 0.92 -6.04 3.61 +UA -4.62 -5.98 -6.59 1.10 -2.61 -7.42 2.32 -4.67 -5.85 0.94 -6.46 -1.22 5.12 +UC -12.65 -8.91 -8.01 -5.72 -7.52 -7.78 -4.67 -4.13 -6.52 -4.79 -11.27 -5.30 -3.15 -3.05 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-4.44 1.33 +U -3.43 -2.52 -3.73 1.96 +H: 1.6093 +E: -0.8976 + + AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU +AA -0.89 +AC -8.43 -0.44 +AG -8.85 -8.34 -0.37 +AU -5.20 -4.12 -6.93 5.17 +CA -10.78 -10.53 -11.20 -7.88 -2.40 +CC -999.00 -8.58 -14.27 -8.97 -10.00 -1.58 +CG -7.20 -7.96 -5.92 -1.18 -4.25 -5.07 5.81 +CU -13.73 -12.37 -11.80 -5.86 -9.94 -8.32 -5.53 -0.93 +GA -7.33 -14.12 -10.33 -8.67 -9.57 -13.04 -8.70 -14.68 -0.60 +GC -6.47 -4.21 -8.93 0.81 -7.76 -4.45 -0.87 -7.09 -6.23 5.93 +GG -10.50 -13.26 -7.29 -7.53 -10.66 -12.36 -5.37 -12.46 -8.89 -5.32 -1.73 +GU -7.82 -6.74 -9.22 -0.68 -9.19 -9.49 -2.84 -6.11 -6.21 -0.02 -5.99 3.88 +UA -5.70 -7.32 -7.74 -0.97 -3.49 -8.77 0.72 -7.49 -6.79 -1.54 -7.72 -3.03 5.40 +UC -12.62 -8.33 -13.31 -7.81 -13.36 -8.48 -7.40 -5.72 -15.00 -5.17 -12.59 -7.34 -5.49 -1.34 +UG -7.39 -9.45 -6.05 -3.18 -6.81 -8.81 0.10 -8.12 -9.83 -2.83 -5.79 -3.77 -0.55 -5.90 3.85 +UU -10.74 -10.34 -9.66 -4.21 -10.90 -7.42 -5.58 -7.09 -14.11 -5.69 -10.34 -5.42 -4.68 -5.43 -5.34 0.50 +H: 4.7497 +E: -6.4455 + diff --git a/src/matrices/RIBOSUM95-95.mat b/src/matrices/RIBOSUM95-95.mat new file mode 100644 index 0000000..1630784 --- /dev/null +++ b/src/matrices/RIBOSUM95-95.mat @@ -0,0 +1,30 @@ +RIBOSUM95-95 + + A C G U +A 2.51 +C -5.56 1.70 +G -5.07 -5.91 1.39 +U -5.06 -3.99 -5.52 2.05 +H: 1.8665 +E: -1.4737 + + AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU +AA -0.89 +AC -8.89 -0.26 +AG -8.50 -10.71 -0.33 +AU -6.76 -5.05 -7.64 5.29 +CA -999.00 -11.41 -13.54 -9.14 -1.46 +CC -999.00 -8.94 -999.00 -10.52 -9.83 -1.20 +CG -12.65 -11.94 -6.91 -3.45 -4.89 -6.23 5.88 +CU -13.62 -999.00 -999.00 -6.53 -10.23 -7.68 -6.17 -0.66 +GA -8.24 -999.00 -9.67 -13.62 -10.42 -14.51 -9.46 -13.59 -0.54 +GC -9.24 -5.21 -10.30 -1.44 -10.45 -5.72 -3.12 -8.28 -6.86 6.00 +GG -11.24 -11.17 -9.29 -9.06 -10.05 -12.80 -6.49 -15.37 -9.24 -6.07 -1.49 +GU -11.28 -9.05 -11.29 -1.94 -13.10 -10.27 -4.78 -7.09 -7.43 -1.55 -7.79 3.97 +UA -7.33 -10.49 -9.51 -3.31 -4.95 -8.83 -1.40 -9.53 -8.45 -3.87 -16.97 -5.34 5.51 +UC -999.00 -7.79 -11.88 -8.42 -11.46 -9.24 -10.27 -9.28 -999.00 -6.05 -999.00 -10.93 -6.59 -1.07 +UG -9.83 -11.97 -8.80 -5.48 -8.66 -12.47 -1.26 -9.81 -10.61 -4.77 -8.00 -6.35 -1.97 -7.24 4.00 +UU -999.00 -12.30 -12.12 -5.59 -11.75 -999.00 -8.28 -7.83 -999.00 -8.09 -16.09 -7.08 -5.67 -6.05 -6.96 0.58 +H: 5.1321 +E: -46.4133 + diff --git a/src/matrices/RIBOSUM95.mat b/src/matrices/RIBOSUM95.mat new file mode 100644 index 0000000..5b8a61f --- /dev/null +++ b/src/matrices/RIBOSUM95.mat @@ -0,0 +1,30 @@ +RIBOSUM95 + + A C G U +A 1.96 +C -1.33 0.99 +G -0.91 -1.69 0.85 +U -0.97 -0.62 -1.10 1.37 +H: 0.5525 +E: -0.0920 + + AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU +AA -2.84 +AC -8.54 -2.06 +AG -9.17 -9.34 -1.33 +AU -4.96 -1.63 -5.89 4.22 +CA -9.97 -10.36 -10.35 -5.61 -6.19 +CC -13.47 -8.79 -14.75 -2.48 -11.36 -3.69 +CG -3.83 -5.35 -2.56 2.06 -3.14 -5.02 5.22 +CU -11.94 -10.61 -9.50 -4.13 -8.34 -6.95 -4.33 -2.68 +GA -6.95 -7.67 -9.63 -3.86 -7.99 -12.70 -5.85 -7.60 -1.65 +GC -5.18 -2.70 -6.11 2.89 -5.34 -3.70 2.82 -2.20 -2.61 5.50 +GG -9.66 -10.14 -4.36 -4.81 -11.46 -11.71 -4.66 -9.31 -9.51 -4.64 -2.19 +GU -6.42 -4.68 -7.08 0.74 -6.09 -6.99 0.26 -4.45 -6.24 1.43 -5.52 3.31 +UA -2.49 -5.39 -2.84 1.90 -2.90 -6.31 2.96 -4.32 -4.74 1.94 -6.22 0.09 4.71 +UC -11.83 -8.91 -7.96 -4.30 -7.83 -8.56 -4.27 -4.58 -7.14 -4.06 -10.72 -4.57 -3.55 -3.99 +UG -3.65 -7.12 -5.78 -0.37 -6.10 -8.23 1.22 -6.41 -7.63 0.32 -4.28 -1.33 1.05 -4.24 3.18 +UU -8.89 -8.30 -9.54 -2.40 -8.87 -6.51 -3.04 -5.40 -9.79 -2.94 -5.03 -2.63 -1.59 -6.03 -3.68 -0.74 +H: 3.4585 +E: -2.5897 + diff --git a/src/mountain_height b/src/mountain_height new file mode 100644 index 0000000..070f482 Binary files /dev/null and b/src/mountain_height differ diff --git a/src/mountain_height.cpp b/src/mountain_height.cpp new file mode 100644 index 0000000..049439d --- /dev/null +++ b/src/mountain_height.cpp @@ -0,0 +1,172 @@ +#include "mountain_height.h" + + +const int DANGLE=2; +double T= 37.; +double kT = (T + 273.15)*1.98717/1000.; /* kT in kcal/mol */ +int engFlag=2004;//Turner2004; Turner1999 and Andronescu072007 also possible + +void BasePairProbabilities(char * seq , int n, double * mfe, char* mfeStr, double *ensEng,char * argv0, double ** bppr) +{ + readEnergyFile(argv0); + FLT_OR_DBL *bppm; + dangles = DANGLE; + temperature = T; + *mfe = fold(seq,mfeStr); + //printf("seq:%s,temp:%f,d:%d,mfe:%f\n",seq,T,dangleFlag,*mfe); + pf_scale = exp((-*mfe/kT)/n); + //update_pf_params(n); + *ensEng = pf_fold(seq, NULL); + bppm = export_bppm(); + + //double **bppr = new double *[n]; + //for(int i = 0; i < n; i++) + // bppr[i] = new double[n+1]; + for(int i=0;i heightDiff(vector h){ + vector h_diff; + h_diff.push_back(h[0]); + for(int i=1;i expectedModifiedHeight(double ** bppr, int n) +{ + vector h; + for(int i=0;i expectedHeight(double **bppr , int n) +{ + vector h; + int i; + for(i=0;i & h){ + printf("["); + int i; + for(i=0;i& h){ + char buff[50000]=""; + int i; + sprintf(buff+strlen(buff),"["); + for(i=0;i +#include +#include +#include +#include "aux.h" +extern "C"{ +#include "utils.h" +#include "fold_vars.h" +#include "fold.h" +#include "part_func.h" +#include "RNAstruct.h" +#include "cofold.h" +#include "part_func_co.h" +#include "read_epars.h" +#include "alifold.h" +} + +using namespace std; + + +void BasePairProbabilities(char * seq , int n, double * mfe, char* mfeStr, double *ensEng,char* argv0, double ** bppr); +vector expectedModifiedHeight(double ** bppr, int n); +vector expectedHeight(double **bppr , int n); +vector heightDiff(vector h); +void readEnergyFile(char * argv0); +double basePairProbability(double **bppr , int n); +void printHeights(const vector &h); +string sprintHeights(const vector & h); +void runAlifold(const char ** seqs , char * str, double &mfe); +#endif /* MOUNTAINHEIGHT_H_ */ diff --git a/src/multi_align.cpp b/src/multi_align.cpp new file mode 100644 index 0000000..cc0132f --- /dev/null +++ b/src/multi_align.cpp @@ -0,0 +1,397 @@ +/* + * multialign.cpp + * + * Created on: Dec 15, 2016 + * Author: Amir Bayegan + */ + +#include "multi_align.h" +//#define DEBUG + +vector multi_align(const Arguments &args){ + int i,j,n,l,MAXL; + const int SEQNUM = args.seqs.size(); + //---get length of the longest sequence + MAXL = -1; + for (i = 0; i < SEQNUM; ++i) { + l = args.seqs[i].length(); + if (l>MAXL) { + MAXL = l; + } + } + + char * s = new char[MAXL+1]; + char * mfeStr = new char[MAXL+1]; + double ** bppr = allocate2DdoubleArray(MAXL+1,MAXL+1) ; + double MFE,ensEng; + double ** pairwiseSim= allocate2DdoubleArray(SEQNUM,SEQNUM); + vector h; + vector > inc_h; + vector > raw_h; + vector bpvec;//average base pairing probability of sequences + + double bp; + double shift_str=1,mul_seq=1; + + vector > profvec; + for(i = 0; i < SEQNUM; ++i){ + profvec.push_back(vector(SEQNUM)); + for (j = 0; j < SEQNUM; ++j){ + profvec[i].push_back(Profile()); + } + } + + + for (i = 0; i < SEQNUM; ++i) { + n = args.seqs[i].length(); + //fold and get base pairing probabilities + strcpy(s,args.seqs[i].c_str()); + BasePairProbabilities(s,n,&MFE,mfeStr,&ensEng,args.argv0,bppr); + + bp=0; + for(j=0;jprofile.getSeqs(); +} + +double seqIdentity(string seq1,string seq2){ + int i,n; + int ident=0; + if(seq1.length()!=seq2.length()){ + reportErr("Error in pairwiseIdentity()! Sequences do not have the same length"); + } + n = seq1.length(); + for (i = 0; i < n; ++i) { + if(seq1[i]==seq2[i] && seq1[i]!='-' && seq2[i]!='-'){ + ident+=1; + } + } + return double(ident)/n; +} + + +void BuildPairwiseDistanceMatrix(vector > heights, vector bpvec, double shift_str, double mul_seq ,int SEQNUM, Arguments args, double ** pairwiseSim, vector > &profvec ){ + int i,j,k,l; + + + vector > htmp; + vector stmp; + vector idtmp; + vector > pos; + + for(i = 0; i < SEQNUM; ++i){ + for (j = i+1; j < SEQNUM; ++j) { + pos.clear();htmp.clear();idtmp.clear();stmp.clear(); + htmp.push_back(heights[i]); + stmp.push_back(args.seqs[i]); + idtmp.push_back(args.ids[i]); + vector posi; + posi.push_back(0); + posi.push_back(args.seqs[i].length()); + pos.push_back(posi); + Profile pi(stmp,idtmp,htmp,pos,bpvec[i]); + + pos.clear();htmp.clear();idtmp.clear();stmp.clear(); + htmp.push_back(heights[j]); + stmp.push_back(args.seqs[j]); + idtmp.push_back(args.ids[j]); + vector posj; + posj.push_back(0); + posj.push_back(args.seqs[i].length()); + pos.push_back(posj); + Profile pj(stmp,idtmp,htmp,pos,bpvec[j]); + args.aln_type='g'; + ProfileAligner pairaln= ProfileAligner(pi,pj,args,shift_str,mul_seq); + profvec[i][j] = pairaln.align(); + + + + //pairwiseDist[i][j] = 1.0-seqIdentity(profvec[i][j].getSeqs()[0],profvec[i][j].getSeqs()[1]); + pairwiseSim[i][j] = pairaln.getScore(); + pairwiseSim[j][i] = pairwiseSim[i][j]; + //printf("D(%d,%d)=%f\n",i,j,pairaln.getScore()); + //pairaln.printAlignment("clustal"); + } + } + //for(int i=0;i > & profvec, vector bpvec, double shift_str, double mul_seq, int N, int weighted, const vector > & heights ,const Arguments &args ){ + /*------------------------------------------------------ + Declarations + -------------------------------------------------------*/ + int ch; + int i_size, j_size; + /* size of i-th and j-th clusters to be amalgamated*/ + + int num; /* number of clusters */ + int i,i_index; /* i_index index of new cluster to amalgamate */ + int j,j_index; /* j_index index of new cluster to amalgamate */ + float d,dmax; /* used to find closest clusters to amalgamate */ + vector c(N); /* c[i] is tree of i-th cluster */ + Node * p; + + double ** E = allocate2DdoubleArray(N,N); + ProfileAligner *f; /*used to save and print the final alignment*/ + /*------------------------------------------- + E[i][j] distance between i-th and j-th cluster, + updated upon amalgamation of clusters. + copy D into E, E[i][j] distance between i-th + and j-th cluster. + -------------------------------------------*/ + E = D; + /*------------------------------------------- + Initialize clusters and cluster sizes. + -------------------------------------------*/ + for (i=0;ileaf = 1; + c[i]->depth = 0; + c[i]->dist = 0; + c[i]->index = i; + c[i]->size = 1; + c[i]->left = NULL; + c[i]->right = NULL; + vector > htmp; + vector stmp; + vector idtmp; + vector > pos; + htmp.push_back(heights[i]); + stmp.push_back(args.seqs[i]); + idtmp.push_back(args.ids[i]); + vector pos0; + pos0.push_back(0); + pos0.push_back(args.seqs[i].length()); + pos.push_back(pos0); + Profile p0(stmp,idtmp,htmp,pos,bpvec[i]); + c[i]-> profile = p0; + } + + /*------------------------------------------- + Using E[i][j] find the closest 2 clusters, amalgamate, + update array of clusters, size of clusters, and E[i][j]'s. + Repeatedly do this, until there is only 1 cluster left. + -------------------------------------------*/ + num = N; + while ( num > 1 ) + { + dmax = -INF; + for (i=0;i dmax ) + { + dmax = d; + i_index = i; + j_index = j; + } + } + } + /*------------------------------------------- + Create new node, left child is c[i], right child is c[j]. + Value of p node is distance between c[i] and c[j] clusters. + c[i] is now p, the amalgamated cluster (ileaf = 0; + p->depth = 1 + MAX(c[i]->depth,c[j]->depth); + p->dist = E[i][j]; + p->index = -1; /* important */ + i_size = c[i]->size; /* size of i-th cluster */ + j_size = c[j]->size; /* size of j-th cluster */ + p->size = i_size + j_size; + p->left = c[i]; + p->right = c[j]; + + + if(c[i]->profile.getNumberOfSeqs()==1 && c[j]->profile.getNumberOfSeqs()==1 && args.aln_type=='g'){//reuse the pairwise alignments + p->profile=profvec[i][j]; + //p->profile.printProfile("clustal"); + //for (int i=0; i< p->profile.getSumOfHeights().size();++i) + //printf("%.2f ",p->profile.getSumOfHeights()[i]); + //printf("\n"); + } + else{ + f = new ProfileAligner(c[i]->profile, c[j]->profile,args, shift_str, mul_seq); + p->profile = f->align(); + //p->profile.printProfile("clustal"); + //for (int i=0; i< p->profile.getSumOfHeights().size();++i) + //printf("%.2f ",p->profile.getSumOfHeights()[i]); + //printf("\n"); + } + c[i] = p; + c[j] = NULL; + num--; + /*------------------------------------------- + Update E. + -------------------------------------------*/ + for (j=0;jprintAlignment(args.outformat); + return c[i_index]; +} + + + +//void MultiAlign::WriteNewick(Node * p){ +// p. +// +//} + +/*------------------------------------------- +print phylogeny tree. When call, n should be depth +of tree. +-------------------------------------------*/ +void printTree( Node * p, int n) +{ + int TABSIZE=8; + int i; + int depth( Node * ); + + if ( p->leaf == 1 ) + { + for (i=0;iindex); + } + else + { + printTree(p->right,n+1); + /*----------------- vertical bar towards parent ---*/ + for (i=0;idist/(float) 2); + /* ancestor is half distance from children */ + + /*----------------- vertical bar towards parent ---*/ + for (i=0;ileft,n+1); + } +} + +void scaleSimilarityScores(const Arguments &args, const vector & bpvec,double &shift_str, double &mul_seq){ + double bpl,bp; + double sum=0; + int n=bpvec.size(); + double nucpr[4]={0,0,0,0}; + int m=0; + double mu_seq,std_seq,mu_str,std_str; + + //compute average base pairing probability over all sequences + for (int i = 0; i < n; ++i) { + sum+=bpvec[i]; + } + bp = sum/n; + + //compute nucleotide probability assuming a single long sequence is given + for (int i = 0; i < n; ++i) { + for (int j = 0; j < args.seqs[i].length(); ++j) { + nucpr[char2num(args.seqs[i][j])]++; + m++; + } + } + for (int i = 0; i < 4; ++i){ + nucpr[i]/=m; + } + + //compute mean and std of sequence similarity scores + for (int nuc0 = 0; nuc0 < 4; ++nuc0) { + for (int nuc1 = 0; nuc1 < 4; ++nuc1) { + mu_seq += nucpr[nuc0]*nucpr[nuc1]*args.subMat[nuc0][nuc1]; + } + } + for (int nuc0 = 0; nuc0 < 4; ++nuc0) { + for (int nuc1 = 0; nuc1 < 4; ++nuc1) { + std_seq+= nucpr[nuc0]*nucpr[nuc1]*(args.subMat[nuc0][nuc1]-mu_seq)*(args.subMat[nuc0][nuc1]-mu_seq); + } + } + std_seq = sqrt(std_seq); + + //compute mean and std of structure similarity scores + bpl=bp/2.0;//base pairing to the left or right + mu_str = -1.0*(4*bpl*(1.0-bp))+ //#"(" with "." or ")" with "." + -2.0*(2*bpl*bpl); // #"(" with ")" + + + std_str = (-1.0 - mu_str)*(-1.0 - mu_str)*(4*bpl*(1.0-bpl))+ //#"(" with "." or ")" with "." + (-2.0 - mu_str)*(-2.0 - mu_str)*(2*bpl*bpl); // #"(" with ")" + + std_str= sqrt(std_str); + + if (!equal(std_seq,0.0) and !equal(std_str,0.0)){ + // mult_seq = (stdStr/stdSeq)*(str_weight/(1-str_weight)); + mul_seq = std_str/std_seq; + } + shift_str = mul_seq*mu_seq - mu_str; + sprintf(outtxt+strlen(outtxt),"#Scaling factors:multiplication=%f,shift=%f\n",mul_seq,shift_str); + sprintf(outtxt+strlen(outtxt),"#Mean: structure:%f,sequence=%f\n",mu_str,mu_seq); + sprintf(outtxt+strlen(outtxt),"#Std: structure=%f,sequence=%f\n\n",std_str,std_seq); +} + + + + + + + + diff --git a/src/multi_align.h b/src/multi_align.h new file mode 100644 index 0000000..ebb6b60 --- /dev/null +++ b/src/multi_align.h @@ -0,0 +1,47 @@ +/* + * multialign.h + * + * Created on: Dec 15, 2016 + * Author: Amir Bayegan + */ + + +#ifndef MULTIALIGN_H_ +#define MULTIALIGN_H_ + +#include +#include +#include +#include "pair_align.h" +#include "aux.h" +#include "profile_aligner.h" +#include "mountain_height.h" +#include "profile.h" + +using namespace std; + +#define MAX(x,y) ( (x)>(y) ? (x) : (y) ) + +vector multialign(const Arguments &args); +double pairwiseDistance(string ,string); + +struct Node +{ + int leaf; /* leaf = 1 if true, else 0 */ + int depth; /* depth of leaf is 0 */ + float dist; /* dist is distance between left, right clusters */ + int index; /* name of species, if node is leaf, else -1 */ + int size; /* size of current cluster */ + struct Node *left; + struct Node *right; + Profile profile; + //Node(); + //Node(const Node & that); +}; +vector multi_align(const Arguments &args); +double seqIdentity(string seq1,string seq2); +void BuildPairwiseDistanceMatrix(vector > heights, vector bpvec, double shift_str, double mul_seq ,int SEQNUM, Arguments args, double ** pairwiseDist, vector > &profvec ); +Node * UPGMA(double ** D, vector > &profvec, vector bpvec,double shift_str, double mul_seq, int N, int weighted, const vector > & heights ,const Arguments &args ); +void printTree( Node * p, int n); +void scaleSimilarityScores(const Arguments &args , const vector & bpvec,double &shift_str, double &mul_seq); +#endif /* MULTIALIGN_H_ */ diff --git a/src/pair_align.cpp b/src/pair_align.cpp new file mode 100644 index 0000000..351be41 --- /dev/null +++ b/src/pair_align.cpp @@ -0,0 +1,904 @@ +#include "pair_align.h" + + +Alignment::Alignment(string seq1,string seq2,const vector &h1 ,const vector &h2, double b1, double b2, const Arguments &args) { + seq1_raw = seq1; + seq2_raw = seq2; + len1_raw = seq1_raw.length(); + len2_raw = seq2_raw.length(); + id1= args.ids[0]; + id2 = args.ids[1]; + len_aln=0; + gap_init = args.gap_init; + gap_ext = args.gap_ext; + gap_init_str = args.gap_init_str; + gap_ext_str = args.gap_ext_str; + str_weight = args.str_weight; + aln_type = args.aln_type; + seq1_aln = ""; + seq2_aln = ""; + vector< vector > tmp0(len1_raw+1, vector(len2_raw+1,0)); + scoreMatrix_p = tmp0; + scoreMatrix_q = tmp0; + scoreMatrix_r = tmp0; + + vector< vector > tmp1(len1_raw+1, vector(len2_raw+1,'N')); + pathMatrix_p =tmp1; + pathMatrix_q =tmp1; + pathMatrix_r =tmp1; + + h1_raw = h1; + h2_raw = h2; + + max_score=-INF; + aln_start[0]=1;aln_start[1]=1; + aln_stop[0]=len1_raw;aln_stop[1]=len2_raw; + + for (int i=0;i<=3;i++) + for (int j=0;j<=3;j++) + seq_similarity[i][j]=args.subMat[i][j]; + + weighted_gap_init = (1-str_weight)*gap_init + str_weight*(gap_init_str); + weighted_gap_ext = (1-str_weight)*gap_ext + str_weight*(gap_ext_str); + outformat = args.outformat; + fixed_gamma = args.fixed_gamma; + //getBPprobs(); + bp1=b1; + bp2=b2; + scaleScores(); + //print base pair probabilities + //printf("\nbase pair probabilities:\n"); + //printf("SEQ1:\n"); + //for (int i=0; i &h1 ,const vector &h2, + double ** probmat1, double ** probmat2, const Arguments &args) { + seq1_raw = seq1; + seq2_raw = seq2; + len1_raw = seq1_raw.length(); + len2_raw = seq2_raw.length(); + id1= args.ids[0]; + id2 = args.ids[1]; + len_aln=0; + gap_init = args.gap_init; + gap_ext = args.gap_ext; + gap_init_str = args.gap_init_str; + gap_ext_str = args.gap_ext_str; + str_weight = args.str_weight; + aln_type = args.aln_type; + seq1_aln = ""; + seq2_aln = ""; + vector< vector > tmp0(len1_raw+1, vector(len2_raw+1,0)); + scoreMatrix_p = tmp0; + scoreMatrix_q = tmp0; + scoreMatrix_r = tmp0; + + vector< vector > tmp1(len1_raw+1, vector(len2_raw+1,'N')); + pathMatrix_p =tmp1; + pathMatrix_q =tmp1; + pathMatrix_r =tmp1; + + bppr1 = allocate2DdoubleArray(len1_raw,len1_raw); + bppr2 = allocate2DdoubleArray(len2_raw,len2_raw); + bppr1 = probmat1; + bppr2 = probmat2; + + h1_raw = h1; + h2_raw = h2; + + max_score=-INF; + aln_start[0]=1;aln_start[1]=1; + aln_stop[0]=len1_raw;aln_stop[1]=len2_raw; + + for (int i=0;i<=3;i++) + for (int j=0;j<=3;j++) + seq_similarity[i][j]=args.subMat[i][j]; + + weighted_gap_init = (1-str_weight)*gap_init + str_weight*(gap_init_str); + weighted_gap_ext = (1-str_weight)*gap_ext + str_weight*(gap_ext_str); + outformat = args.outformat; + fixed_gamma = args.fixed_gamma; + getBPprobs(); + scaleScores(); + //print base pair probabilities + //printf("\nbase pair probabilities:\n"); + //printf("SEQ1:\n"); + //for (int i=0; i (const Alignment & aln) const{ + return (max_score > aln.max_score); +} + +vector Alignment::getAlignmentPositions(){ + vector pos(4); + pos[0] = aln_start[0];pos[1] = aln_stop[0]; + pos[2] = aln_start[1];pos[3] = aln_stop[1]; + return pos; +} + +double Alignment::getScore(){ + return max_score; +} +string Alignment::getSeq1(){ + return seq1_aln; +} + +string Alignment::getSeq2(){ + return seq2_aln; +} + +int Alignment::getLength(){ + return len_aln; +} +char Alignment::getType(){ + return aln_type; +} + +void Alignment::getBPprobs(){ + //bpppr[i][n] contains probability of i being base paired + int i; + bp1=0.0; + for(i=0;i0 || y>0){ +// printf("%u,%u,%c\n",x,y,matrix); + //NOTE: sequence is 0-indexed but matrices have empty row and columns + if(matrix=='R'){ + seq1_aln+=seq1_raw[x-1]; + seq2_aln+=seq2_raw[y-1]; + h1_aln.push_back(h1_raw[x-1]); + h2_aln.push_back(h2_raw[y-1]); + matrix = pathMatrix_r[x][y]; + x-=1;y-=1; + } + else if(matrix=='P'){ + seq1_aln+=seq1_raw[x-1]; + seq2_aln+='-'; + h1_aln.push_back(h1_raw[x-1]); + h2_aln.push_back('-'); + matrix = pathMatrix_p[x][y]; + x-=1; + } + else if(matrix=='Q'){ + seq1_aln+='-'; + seq2_aln+=seq2_raw[y-1]; + h1_aln.push_back('-'); + h2_aln.push_back(h2_raw[y-1]); + matrix = pathMatrix_q[x][y]; + y-=1; + } + } + len_aln=h1_aln.size(); + reverse(seq1_aln.begin(), seq1_aln.end()); + reverse(seq2_aln.begin(), seq2_aln.end()); + reverse(h1_aln.begin(), h1_aln.end()); + reverse(h2_aln.begin(), h2_aln.end()); +} + +//while(x>0 || y>0){ +//// printf("%u,%u,%c\n",x,y,matrix); +// if(matrix=='R'){ +// seq1_aln+=seq1_raw[x-1]; +// seq2_aln+=seq2_raw[y-1]; +// h1_aln.push_back(h1_raw[x-1]); +// h2_aln.push_back(h2_raw[y-1]); +// matrix = pathMatrix_r[x][y]; +// x-=1;y-=1; +// } +// else if(matrix=='P'){ +// seq1_aln+=seq1_raw[x-1]; +// seq2_aln+='-'; +// h1_aln.push_back(h1_raw[x-1]); +// h2_aln.push_back('-'); +// matrix = pathMatrix_p[x][y]; +// x-=1; +// } +// else if(matrix=='Q'){ +// seq1_aln+='-'; +// seq2_aln+=seq2_raw[y-1]; +// h1_aln.push_back('-'); +// h2_aln.push_back(h2_raw[y-1]); +// matrix = pathMatrix_q[x][y]; +// y-=1; +// } +// } +// len_aln=h1_aln.size(); +// reverse(seq1_aln.begin(), seq1_aln.end()); +// reverse(seq2_aln.begin(), seq2_aln.end()); +// reverse(h1_aln.begin(), h1_aln.end()); +// reverse(h2_aln.begin(), h2_aln.end()); +//} + +//#ifdef DEBUG +// printf("P:\n"); +// printMatrix1(scoreMatrix_p,len1_raw+1,len2_raw+1); +// printMatrix(pathMatrix_p,len1_raw+1,len2_raw+1); +// printf("Q:\n"); +// printMatrix1(scoreMatrix_q,len1_raw+1,len2_raw+1); +// printMatrix(pathMatrix_q,len1_raw+1,len2_raw+1); +// printf("R:\n"); +// printMatrix1(scoreMatrix_r,len1_raw+1,len2_raw+1); +// printMatrix(pathMatrix_r,len1_raw+1,len2_raw+1); +//#endif + +void Alignment::buildSmithWatermanScoreMatrix(){ + //-----------initialize matrices + scoreMatrix_p[0][0]=0; + scoreMatrix_q[0][0]=0; + scoreMatrix_r[0][0]=0; + for(int i=1;i<=len1_raw;i++){ + scoreMatrix_p[i][0]= 0; + scoreMatrix_q[i][0]= 0; + scoreMatrix_r[i][0]= 0; + pathMatrix_p[i][0]='P'; + pathMatrix_q[i][0]='N'; //N is not used + pathMatrix_r[i][0]='N'; + } + for(int i=1;i<=len2_raw;i++){ + scoreMatrix_p[0][i]= 0; + scoreMatrix_q[0][i]= 0; + scoreMatrix_r[0][i]= 0; + pathMatrix_q[0][i]='Q'; + pathMatrix_p[0][i]='N'; + pathMatrix_r[0][i]='N'; + } + + //------Fill the matrices + char ptr; + double maxv; + for(int i=0;i max_score){ + max_score = scoreMatrix_p[i][j]; + x=i;y=j; + matrix='P'; + } + if (scoreMatrix_q[i][j] > max_score){ + max_score = scoreMatrix_q[i][j]; + x=i;y=j; + matrix='Q'; + } + if (scoreMatrix_r[i][j] > max_score){ + max_score = scoreMatrix_r[i][j]; + x=i;y=j; + matrix='R'; + } + } + } + aln_stop[0]=x;aln_stop[1]=y; + score = max_score; +// if(matrix>0){ +// seq1_aln+=seq1_raw[x-1]; +// seq2_aln+=seq2_raw[y-1]; +// h1_aln.push_back(h1_raw[x-1]); +// h2_aln.push_back(h2_raw[y-1]); +// x--;y--; +// } + while(score>0){ + if(matrix=='R'){ + seq1_aln+=seq1_raw[x-1]; + seq2_aln+=seq2_raw[y-1]; + h1_aln.push_back(h1_raw[x-1]); + h2_aln.push_back(h2_raw[y-1]); + matrix = pathMatrix_r[x][y]; + x-=1;y-=1; + } + else if(matrix=='P'){ + seq1_aln+=seq1_raw[x-1]; + seq2_aln+='-'; + h1_aln.push_back(h1_raw[x-1]); + h2_aln.push_back('-'); + matrix = pathMatrix_p[x][y]; + x-=1; + } + else if(matrix=='Q'){ + seq1_aln+='-'; + seq2_aln+=seq2_raw[y-1]; + h1_aln.push_back('-'); + h2_aln.push_back(h2_raw[y-1]); + matrix = pathMatrix_q[x][y]; + y-=1; + } + if(matrix=='P'){ + score=scoreMatrix_p[x][y]; + } + else if(matrix=='Q'){ + score = scoreMatrix_q[x][y]; + } + else if(matrix=='R'){ + score = scoreMatrix_r[x][y]; + } + + + } + aln_start[0]=x+1;aln_start[1]=y+1; + len_aln=h1_aln.size(); + //printf("****%s\n%s\n;",seq1_aln.c_str(),seq2_aln.c_str()); + reverse(seq1_aln.begin(), seq1_aln.end()); + reverse(seq2_aln.begin(), seq2_aln.end()); + reverse(h1_aln.begin(), h1_aln.end()); + reverse(h2_aln.begin(), h2_aln.end()); + //printf("****%s\n%s\n;",seq1_aln.c_str(),seq2_aln.c_str()); +} + +void Alignment::buildSemiGlobalScoreMatrix(){ + //-----------initialize matrices + scoreMatrix_p[0][0]=0; + scoreMatrix_q[0][0]=0; + scoreMatrix_r[0][0]=0; + for(int i=1;i<=len1_raw;i++){ + scoreMatrix_p[i][0]= -INF; + scoreMatrix_q[i][0]= gap(i); + scoreMatrix_r[i][0]= -INF; + pathMatrix_p[i][0]='Q'; + pathMatrix_q[i][0]='N'; //N is not used + pathMatrix_r[i][0]='N'; + } + for(int i=1;i<=len2_raw;i++){ + scoreMatrix_p[0][i]= 0; + scoreMatrix_q[0][i]= -INF; + scoreMatrix_r[0][i]= -INF; + pathMatrix_q[0][i]='P'; + pathMatrix_p[0][i]='N'; + pathMatrix_r[0][i]='N'; + } + //------Fill the matrices + char ptr; + for(int i=0;i max_score){ + max_score = scoreMatrix_p[len1_raw][i]; + x=len1_raw;y=i; + matrix='P'; + } + if (scoreMatrix_q[len1_raw][i] > max_score){ + max_score = scoreMatrix_q[len1_raw][i]; + x=len1_raw;y=i; + matrix='Q'; + } + if (scoreMatrix_r[len1_raw][i] > max_score){ + max_score = scoreMatrix_r[len1_raw][i]; + x=len1_raw;y=i; + matrix='R'; + } + } + aln_stop[0]=x;aln_stop[1]=y; + score = max_score; + + while(x>0){ + //printf("%u,%u,%c\n",x,y,matrix); + if(matrix=='R'){ + seq1_aln+=seq1_raw[x-1]; + seq2_aln+=seq2_raw[y-1]; + h1_aln.push_back(h1_raw[x-1]); + h2_aln.push_back(h2_raw[y-1]); + matrix = pathMatrix_r[x][y]; + x-=1;y-=1; + } + else if(matrix=='P'){ + seq1_aln+=seq1_raw[x-1]; + seq2_aln+='-'; + h1_aln.push_back(h1_raw[x-1]); + h2_aln.push_back('-'); + matrix = pathMatrix_p[x][y]; + x-=1; + } + else if(matrix=='Q'){ + seq1_aln+='-'; + seq2_aln+=seq2_raw[y-1]; + h1_aln.push_back('-'); + h2_aln.push_back(h2_raw[y-1]); + matrix = pathMatrix_q[x][y]; + y-=1; + } + } + aln_start[0]=x+1;aln_start[1]=y+1; + len_aln=h1_aln.size(); + reverse(seq1_aln.begin(), seq1_aln.end()); + reverse(seq2_aln.begin(), seq2_aln.end()); + reverse(h1_aln.begin(), h1_aln.end()); + reverse(h2_aln.begin(), h2_aln.end()); +} + +float Alignment::gap(int k){ + if (k<=0) + return 0; + else + return (1-str_weight)*(gap_init+gap_ext*(k-1)) + str_weight*(gap_init_str+gap_ext_str*(k-1) + (shift_str*k)/2.0);//maximum score of structure similarity is SHIFT +} + + +double Alignment::similarity(int i , int j, bool fixed_gamma){ + double Gamma; + float str_sim; + float scaled_str_sim; + + int x = char2num(seq1_raw[i]); + int y = char2num(seq2_raw[j]); + + if(fixed_gamma) + Gamma = str_weight; + else + Gamma = ((1-bppr1[i][len1_raw]) + (1-bppr2[j][len2_raw]))/2.0; + + scaled_str_sim = -fabs(h1_raw[i]-h2_raw[j]) + shift_str; + double dist = (Gamma*scaled_str_sim +(1-Gamma)*seq_similarity[x][y]*mult_seq); + //printf("%d,%d : %.2f,%.2f,%.2f,%.2f\n",i,j,str_sim,scaled_str_sim,dist,Gamma); + return dist; +} + + +void Alignment::computeQuality(){ + for (int i=0;i nucpr1, nucpr2; + double mu_seq=0.0,std_seq=0.0,mu_str=0.0,std_str=0.0; + mult_seq=1.0;shift_str=1.0; + getNucleotideProbabilities(seq1_raw,nucpr1); + getNucleotideProbabilities(seq2_raw,nucpr2); + computeMeanStdSeqScores(nucpr1,nucpr2,mu_seq,std_seq); + computeMeanStdStrScores(nucpr1,nucpr2,mu_str,std_str); + //printf("museq=%f;stdseq=%f\n",mu_seq,std_seq); + //printf("mustr=%f;stdstr=%f\n",mu_str,std_str); + if (!equal(std_seq,0.0) and !equal(std_str,0.0)){ + mult_seq = std_str/std_seq; + } + shift_str = mult_seq*mu_seq - mu_str; + //printf("mul=%f;shift=%f\n",mult_seq,shift_str); + return; +} + + +void Alignment::computeMeanStdSeqScores(vector p,vector q, double & mu, double & std){ + int i,j; + for(i=0;i p,vector q, double & mu, double & std){ + //Assuming heights of a fixed structure(not the ensemble) structure similarity can be -2,-1,0. + int i,j; + //printf("i:%d,j:%d,bp1:%f,bp2:%f\n",i,j,bp1,bp2); + + double pl1=bp1/2.0,pl2=bp2/2.0; + mu = -1.0*(pl1*(1.0-bp2) + pl2*(1.0-bp1) + pl1*(1.0-bp2) + pl2*(1.0-bp1))+ //#"(" with "." or ")" with "." + -2.0*(pl1*pl2 + pl1*pl2); // #"(" with ")" + std = sqrt((pl1*pl2 + pl1*pl2 + (1.0-bp1)*(1-bp2))*(-mu)*(-mu) + //if the score is 0 + (pl1*(1.0-bp2) + pl2*(1.0-bp1) + pl1*(1.0-bp2) + pl2*(1.0-bp1))*(-1-mu)*(-1-mu)+ //if the score is -1 + (pl1*pl2 + pl1*pl2)*(-2-mu)*(-2-mu));//if the score is -2 + return; +} + + +void Alignment::printAlignment(){ + string tmpstr1,tmpstr2; + int gapnum1,gapnum2; + char tmp1[2000]; + char tmp2[2000]; + string hh1="",hh2=""; + //printf("#%s: %s\n",id1.c_str(),seq1_raw.c_str()); + //printf("#%s: %s\n",id2.c_str(),seq2_raw.c_str()); + printf("\n#Scaling factors:\nmultiplication:%f\nshift:%f \n",mult_seq,shift_str); + printf("\n#Score: %.2f\n\n",max_score); + //print alignment + printf("\n#Alignment\n"); + if(outformat=="clustal"){ + int c = len_aln / LINLEN; + int d = len_aln % LINLEN; + int offset1 = aln_start[0]; + int offset2 = aln_start[1]; + int start=0; + for (int i=1;i<=c;i++){ + tmpstr1 = seq1_aln.substr(start,LINLEN); + gapnum1 = count(tmpstr1.begin(), tmpstr1.end(), '-'); + tmpstr2 = seq2_aln.substr(start,LINLEN); + gapnum2 = count(tmpstr2.begin(), tmpstr2.end(), '-'); + + printf("%-15s %-5d %s %-5d\n",id1.c_str(),offset1,seq1_aln.substr(start,LINLEN).c_str(),offset1+LINLEN-1-gapnum1); + printf("%-20s %s \n" ,"",quality.substr(start,LINLEN).c_str()); + printf("%-15s %-5d %s %-5d\n\n",id2.c_str(),offset2,seq2_aln.substr(start,LINLEN).c_str(),offset2+LINLEN-1-gapnum2); + start+=LINLEN; + offset1+=LINLEN-gapnum1; + offset2+=LINLEN-gapnum2; + } + if(d>0){ + tmpstr1 = seq1_aln.substr(start,d); + gapnum1 = count(tmpstr1.begin(), tmpstr1.end(), '-'); + tmpstr2 = seq2_aln.substr(start,d); + gapnum2 = count(tmpstr2.begin(), tmpstr2.end(), '-'); + printf("%-15s %-5d %s %-5d\n",id1.c_str(),offset1,seq1_aln.substr(start,d).c_str(),offset1+d-1-gapnum1); + printf("%-20s %s \n" ,"",quality.substr(start,d).c_str()); + printf("%-15s %-5d %s %-5d\n\n",id2.c_str(),offset2,seq2_aln.substr(start,d).c_str(),offset2+d-1-gapnum2); + printf("\n"); + } + } + else if(outformat=="fasta"){ + int c = len_aln / LINLEN; + int d = len_aln % LINLEN; + int start=0; + printf(">%s\n",id1.c_str() ); + for (int i=1;i<=c;i++){ + printf("%s\n",seq1_aln.substr(start,LINLEN).c_str()); + start+=LINLEN; + } + if(d>0){ + printf("%s\n",seq1_aln.substr(start,LINLEN).c_str()); + } + start=0; + printf(">%s\n",id2.c_str() ); + for (int i=1;i<=c;i++){ + printf("%s\n",seq2_aln.substr(start,LINLEN).c_str()); + start+=LINLEN; + } + if(d>0){ + printf("%s\n",seq2_aln.substr(start,LINLEN).c_str()); + } + } +} + +string Alignment::sprintAlignment(){ + string tmpstr1,tmpstr2; + int gapnum1,gapnum2; + char buff[10000]=""; + string com = "#"; + const int LINLEN=60; + char tmp1[2000]=""; + char tmp2[2000]=""; + string hh1="",hh2=""; + + sprintf(buff+strlen(buff),"\n#Scaling factors:\nmultiplication:%f\nshift:%f \n",mult_seq,shift_str); + sprintf(buff+strlen(buff),"\n#Score: %.2f\n\n",max_score); + + //print alignment + sprintf(buff+strlen(buff),"\n#Alignment\n"); + if(outformat=="clustal"){ + sprintf(buff+strlen(buff),"CLUSTALW\n\n"); + int c = len_aln / LINLEN; + int d = len_aln % LINLEN; + int offset1 = aln_start[0]; + int offset2 = aln_start[1]; + int start=0; + for (int i=1;i<=c;i++){ + tmpstr1 = seq1_aln.substr(start,LINLEN); + gapnum1 = count(tmpstr1.begin(), tmpstr1.end(), '-'); + tmpstr2 = seq2_aln.substr(start,LINLEN); + gapnum2 = count(tmpstr2.begin(), tmpstr2.end(), '-'); + + sprintf(buff+strlen(buff),"%-15s %s %-5d\n",id1.c_str(),seq1_aln.substr(start,LINLEN).c_str(),offset1+LINLEN-1-gapnum1); + sprintf(buff+strlen(buff),"%-15s %s %-5d\n\n",id2.c_str(),seq2_aln.substr(start,LINLEN).c_str(),offset2+LINLEN-1-gapnum2); + + //sprintf(buff+strlen(buff),"%-15s %-5d %s %-5d\n",id1.c_str(),offset1,seq1_aln.substr(start,LINLEN).c_str(),offset1+LINLEN-1-gapnum1); + //sprintf(buff+strlen(buff),"%-20s %s \n" ,"",quality.substr(start,LINLEN).c_str()); + //sprintf(buff+strlen(buff),"%-15s %-5d %s %-5d\n\n",id2.c_str(),offset2,seq2_aln.substr(start,LINLEN).c_str(),offset2+LINLEN-1-gapnum2); + + start+=LINLEN; + offset1+=LINLEN-gapnum1; + offset2+=LINLEN-gapnum2; + } + if(d>0){ + tmpstr1 = seq1_aln.substr(start,d); + gapnum1 = count(tmpstr1.begin(), tmpstr1.end(), '-'); + tmpstr2 = seq2_aln.substr(start,d); + gapnum2 = count(tmpstr2.begin(), tmpstr2.end(), '-'); + sprintf(buff+strlen(buff),"%-15s %s %-5d\n",id1.c_str(),seq1_aln.substr(start,d).c_str(),offset1+d-1-gapnum1); + sprintf(buff+strlen(buff),"%-15s %s %-5d\n\n",id2.c_str(),seq2_aln.substr(start,d).c_str(),offset2+d-1-gapnum2); + //sprintf(buff+strlen(buff),"%-15s %-5d %s %-5d\n",id1.c_str(),offset1,seq1_aln.substr(start,d).c_str(),offset1+d-1-gapnum1); + //sprintf(buff+strlen(buff),"%-20s %s \n" ,"",quality.substr(start,d).c_str()); + //sprintf(buff+strlen(buff),"%-15s %-5d %s %-5d\n\n",id2.c_str(),offset2,seq2_aln.substr(start,d).c_str(),offset2+d-1-gapnum2); + + sprintf(buff+strlen(buff),"\n"); + } + } + else if(outformat=="fasta"){ + int c = len_aln / LINLEN; + int d = len_aln % LINLEN; + int start=0; + sprintf(buff+strlen(buff),">%s\n",id1.c_str() ); + for (int i=1;i<=c;i++){ + sprintf(buff+strlen(buff),"%s\n",seq1_aln.substr(start,LINLEN).c_str()); + start+=LINLEN; + } + if(d>0){ + sprintf(buff+strlen(buff),"%s\n",seq1_aln.substr(start,LINLEN).c_str()); + } + start=0; + sprintf(buff+strlen(buff),">%s\n",id2.c_str() ); + for (int i=1;i<=c;i++){ + sprintf(buff+strlen(buff),"%s\n",seq2_aln.substr(start,LINLEN).c_str()); + start+=LINLEN; + } + if(d>0){ + sprintf(buff+strlen(buff),"%s\n",seq2_aln.substr(start,LINLEN).c_str()); + } + } + return buff; +} + diff --git a/src/pair_align.h b/src/pair_align.h new file mode 100644 index 0000000..8a575c9 --- /dev/null +++ b/src/pair_align.h @@ -0,0 +1,103 @@ +#include +#include +#include +#include +#include +#include +#include +#include "aux.h" +#include "arguments.h" + +#ifndef ALIGNMENT_H_ +#define ALIGNMENT_H_ + +using namespace std; + +const int INF = numeric_limits::max(); + +class Alignment { + +public: + Alignment(); + Alignment(string,string,const vector &, const vector &, + double **, double **,const Arguments & args); + Alignment(string,string,const vector &, const vector &,double , double,const Arguments & args); + void printAlignment(); + string sprintAlignment(); + void computeQuality(); + void align(); + virtual ~Alignment(); + + char getType(); + string getSeq1(); + string getSeq2(); + vector getAlignmentPositions(); + int getLength(); + bool operator < (const Alignment &) const; + bool operator > (const Alignment &) const; + double getScore(); + + //Alignment& operator=(const Alignment& that); +private: + char aln_type; + string seq1_raw; + string seq2_raw; + int len1_raw; + int len2_raw; + vector h1_raw; + vector h2_raw; + string id1,id2; + + string seq1_aln; + string seq2_aln; + int aln_start[2]; + int aln_stop[2]; + vector h1_aln; + vector h2_aln; + double ** bppr1; + double ** bppr2; + + int len_aln; + vector prob_profile; + float gap_init; + float gap_ext; + float gap_init_str; + float gap_ext_str; + float weighted_gap_init; + float weighted_gap_ext; + float str_weight; + float shift_str; + float mult_seq; + + vector > scoreMatrix_p; + vector > scoreMatrix_q; + vector > scoreMatrix_r; + + vector > pathMatrix_p; + vector > pathMatrix_q; + vector > pathMatrix_r; + + const char * sub_mat_name; + float seq_similarity[4][4]; + double max_score; + string quality; + float gap(int); + string outformat; + bool fixed_gamma; + double bp1,bp2; //base pairing probability in seq1,seq2 + + + void buildNeedlemanWunschScoreMatrix(); + void backtrackNeedlemanWunsch(); + void buildSmithWatermanScoreMatrix(); + void backtrackSmithWaterman(); + void buildSemiGlobalScoreMatrix(); + void backtrackSemiGlobal(); + void scaleScores(); + void computeMeanStdSeqScores(vector p,vector q, double & mu, double & std); + void computeMeanStdStrScores(vector p,vector q, double & mu, double & std); + double similarity(int,int,bool); + void getBPprobs(); +}; + +#endif /* ALIGNMENT_H_ */ diff --git a/src/part_func.h b/src/part_func.h new file mode 100644 index 0000000..afe3799 --- /dev/null +++ b/src/part_func.h @@ -0,0 +1,444 @@ +#ifndef __VIENNA_RNA_PACKAGE_PART_FUNC_H__ +#define __VIENNA_RNA_PACKAGE_PART_FUNC_H__ + +#include "data_structures.h" + +#ifdef __GNUC__ +#define DEPRECATED(func) func __attribute__ ((deprecated)) +#else +#define DEPRECATED(func) func +#endif + + +/** + * \addtogroup pf_fold + * \brief This section provides information about all functions and variables related to + * the calculation of the partition function and base pair probabilities. + * + * Instead of the minimum free energy structure the partition function of all possible structures + * and from that the pairing probability for every possible pair can be calculated, using a dynamic + * programming algorithm as described in \cite mccaskill:1990. + * + * @{ + * \file part_func.h + * \brief Partition function of single RNA sequences + * + * This file includes (almost) all function declarations within the RNAlib that are related to + * Partion function folding... + * @} + */ + +/** + * \brief Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking + * + * Set this variable to 1 prior to a call of pf_fold() to ensure that all matrices needed for stochastic backtracking + * are filled in the forward recursions + * + * \ingroup subopt_stochbt + * + * \see pbacktrack(), pbacktrack_circ + */ +extern int st_back; + +/* +################################################# +# PARTITION FUNCTION COMPUTATION # +################################################# +*/ + +/** + * \brief Compute the partition function \f$Q\f$ for a given RNA sequence + * + * If \a structure is not a NULL pointer on input, it contains on + * return a string consisting of the letters " . , | { } ( ) " denoting + * bases that are essentially unpaired, weakly paired, strongly paired without + * preference, weakly upstream (downstream) paired, or strongly up- + * (down-)stream paired bases, respectively. + * If #fold_constrained is not 0, the \a structure string is + * interpreted on input as a list of constraints for the folding. The + * character "x" marks bases that must be unpaired, matching brackets " ( ) " + * denote base pairs, all other characters are ignored. Any pairs + * conflicting with the constraint will be forbidden. This is usually sufficient + * to ensure the constraints are honored. + * If the parameter calculate_bppm is set to 0 base pairing probabilities will not + * be computed (saving CPU time), otherwise after calculations took place #pr will + * contain the probability that bases \a i and \a j pair. + * + * \ingroup pf_fold + * + * \note The global array #pr is deprecated and the user who wants the calculated + * base pair probabilities for further computations is advised to use the function + * export_bppm() + * \post After successful run the hidden folding matrices are filled with the appropriate Boltzmann factors. + * Depending on whether the global variable #do_backtrack was set the base pair probabilities are already + * computed and may be accessed for further usage via the export_bppm() function. + * A call of free_pf_arrays() will free all memory allocated by this function. + * Successive calls will first free previously allocated memory before starting the computation. + * \see pf_fold(), pf_circ_fold(), bppm_to_structure(), export_bppm(), get_boltzmann_factors(), free_pf_arrays() + * \param[in] sequence The RNA sequence input + * \param[in,out] structure A pointer to a char array where a base pair probability information can be stored in a + * pseudo-dot-bracket notation (may be NULL, too) + * \param[in] parameters Data structure containing the precalculated Boltzmann factors + * \param[in] calculate_bppm Switch to Base pair probability calculations on/off (0==off) + * \param[in] is_constrained Switch to indicate that a structure contraint is passed via the structure argument (0==off) + * \param[in] is_circular Switch to (de-)activate postprocessing steps in case RNA sequence is circular (0==off) + * \return The Gibbs free energy of the ensemble (\f$G = -RT \cdot \log(Q) \f$) in kcal/mol + */ +float pf_fold_par( const char *sequence, + char *structure, + pf_paramT *parameters, + int calculate_bppm, + int is_constrained, + int is_circular); + +/** + * \brief Compute the partition function \f$Q\f$ of an RNA sequence + * + * If \a structure is not a NULL pointer on input, it contains on + * return a string consisting of the letters " . , | { } ( ) " denoting + * bases that are essentially unpaired, weakly paired, strongly paired without + * preference, weakly upstream (downstream) paired, or strongly up- + * (down-)stream paired bases, respectively. + * If #fold_constrained is not 0, the \a structure string is + * interpreted on input as a list of constraints for the folding. The + * character "x" marks bases that must be unpaired, matching brackets " ( ) " + * denote base pairs, all other characters are ignored. Any pairs + * conflicting with the constraint will be forbidden. This is usually sufficient + * to ensure the constraints are honored. + * If #do_backtrack has been set to 0 base pairing probabilities will not + * be computed (saving CPU time), otherwise #pr will contain the probability + * that bases \a i and \a j pair. + * + * \ingroup pf_fold + * + * \note The global array #pr is deprecated and the user who wants the calculated + * base pair probabilities for further computations is advised to use the function + * export_bppm(). + * \note \b OpenMP: + * This function is not entirely threadsafe. While the recursions are working on their + * own copies of data the model details for the recursions are determined from the global + * settings just before entering the recursions. Consider using pf_fold_par() for a + * really threadsafe implementation. + * \pre This function takes its model details from the global variables provided in \e RNAlib + * \post After successful run the hidden folding matrices are filled with the appropriate Boltzmann factors. + * Depending on whether the global variable #do_backtrack was set the base pair probabilities are already + * computed and may be accessed for further usage via the export_bppm() function. + * A call of free_pf_arrays() will free all memory allocated by this function. + * Successive calls will first free previously allocated memory before starting the computation. + * \see pf_fold_par(), pf_circ_fold(), bppm_to_structure(), export_bppm() + * \param sequence The RNA sequence input + * \param structure A pointer to a char array where a base pair probability information can be stored in a pseudo-dot-bracket notation (may be NULL, too) + * \return The Gibbs free energy of the ensemble (\f$G = -RT \cdot \log(Q) \f$) in kcal/mol + */ +float pf_fold(const char *sequence, + char *structure); + +/** + * \brief Compute the partition function of a circular RNA sequence + * + * \ingroup pf_fold + * + * \note The global array #pr is deprecated and the user who wants the calculated + * base pair probabilities for further computations is advised to use the function + * export_bppm(). + * \note \b OpenMP: + * This function is not entirely threadsafe. While the recursions are working on their + * own copies of data the model details for the recursions are determined from the global + * settings just before entering the recursions. Consider using pf_fold_par() for a + * really threadsafe implementation. + * \pre This function takes its model details from the global variables provided in \e RNAlib + * \post After successful run the hidden folding matrices are filled with the appropriate Boltzmann factors. + * Depending on whether the global variable #do_backtrack was set the base pair probabilities are already + * computed and may be accessed for further usage via the export_bppm() function. + * A call of free_pf_arrays() will free all memory allocated by this function. + * Successive calls will first free previously allocated memory before starting the computation. + * \see pf_fold_par(), pf_fold() + * \param[in] sequence The RNA sequence input + * \param[in,out] structure A pointer to a char array where a base pair probability information can be + * stored in a pseudo-dot-bracket notation (may be NULL, too) + * \return The Gibbs free energy of the ensemble (\f$G = -RT \cdot \log(Q) \f$) in kcal/mol + */ +float pf_circ_fold( const char *sequence, + char *structure); + +/** + * \brief Sample a secondary structure from the Boltzmann ensemble according its probability\n + * + * \ingroup subopt_stochbt + * \pre pf_fold_par() or pf_fold() have to be called first to fill the partition function matrices + * + * \param sequence The RNA sequence + * \return A sampled secondary structure in dot-bracket notation + */ +char *pbacktrack(char *sequence); + +/** + * \brief Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability + * + * This function does the same as \ref pbacktrack() but assumes the RNA molecule to be circular + * + * \ingroup subopt_stochbt + * \pre #st_back has to be set to 1 before calling pf_fold() or pf_fold_par() + * \pre pf_fold_par() or pf_circ_fold() have to be called first to fill the partition function matrices + * + * \param sequence The RNA sequence + * \return A sampled secondary structure in dot-bracket notation + */ +char *pbacktrack_circ(char *sequence); + +/** + * \brief Free arrays for the partition function recursions + * + * Call this function if you want to free all allocated memory associated with + * the partition function forward recursion. + * \note Successive calls of pf_fold(), pf_circ_fold() already check if they should free + * any memory from a previous run. + * \note OpenMP notice:
+ * This function should be called before leaving a thread in order to avoid leaking memory + * + * \ingroup pf_fold + * + * \post All memory allocated by pf_fold_par(), pf_fold() or pf_circ_fold() will be free'd + * \see pf_fold_par(), pf_fold(), pf_circ_fold() + */ +void free_pf_arrays(void); + +/** + * \brief Recalculate energy parameters + * + * Call this function to recalculate the pair matrix and energy parameters + * after a change in folding parameters like #temperature + * + * \ingroup pf_fold + * + */ +void update_pf_params(int length); + +/** + * \brief Recalculate energy parameters + * + * \ingroup pf_fold + * + */ +void update_pf_params_par(int length, pf_paramT *parameters); + +/** + * \brief Get a pointer to the base pair probability array + * \ingroup pf_fold + * + * Accessing the base pair probabilities for a pair (i,j) is achieved by + * \code + * FLT_OR_DBL *pr = export_bppm(); + * pr_ij = pr[iindx[i]-j]; + * \endcode + * + * \pre Call pf_fold_par(), pf_fold() or pf_circ_fold() first to fill the base pair probability array + * + * \see pf_fold(), pf_circ_fold(), get_iindx() + * + * \return A pointer to the base pair probability array + */ +FLT_OR_DBL *export_bppm(void); + +/* +################################################# +# OTHER PARTITION FUNCTION RELATED DECLARATIONS # +################################################# +*/ + +/** + * \brief Create a plist from a probability matrix + * + * The probability matrix given is parsed and all pair probabilities above + * the given threshold are used to create an entry in the plist + * + * The end of the plist is marked by sequence positions i as well as j + * equal to 0. This condition should be used to stop looping over its + * entries + * + * \note This function is threadsafe + * \ingroup pf_fold + * \param[out] pl A pointer to the plist that is to be created + * \param[in] probs The probability matrix used for creting the plist + * \param[in] length The length of the RNA sequence + * \param[in] cutoff The cutoff value + */ +void assign_plist_from_pr( plist **pl, + FLT_OR_DBL *probs, + int length, + double cutoff); + +/* this doesn't work if free_pf_arrays() is called before */ +void assign_plist_gquad_from_pr(plist **pl, + int length, + double cut_off); + +char *get_centroid_struct_gquad_pr(int length, + double *dist); + +/** + * \brief Get the pointers to (almost) all relavant computation arrays used in partition function computation + * + * \ingroup pf_fold + * \pre In order to assign meaningful pointers, you have to call pf_fold_par() or pf_fold() first! + * \see pf_fold_par(), pf_fold(), pf_circ_fold() + * \param[out] S_p A pointer to the 'S' array (integer representation of nucleotides) + * \param[out] S1_p A pointer to the 'S1' array (2nd integer representation of nucleotides) + * \param[out] ptype_p A pointer to the pair type matrix + * \param[out] qb_p A pointer to the QB matrix + * \param[out] qm_p A pointer to the QM matrix + * \param[out] q1k_p A pointer to the 5' slice of the Q matrix (\f$q1k(k) = Q(1, k)\f$) + * \param[out] qln_p A pointer to the 3' slice of the Q matrix (\f$qln(l) = Q(l, n)\f$) + * \return Non Zero if everything went fine, 0 otherwise + */ +int get_pf_arrays(short **S_p, + short **S1_p, + char **ptype_p, + FLT_OR_DBL **qb_p, + FLT_OR_DBL **qm_p, + FLT_OR_DBL **q1k_p, + FLT_OR_DBL **qln_p); + +/** + * \brief Get the free energy of a subsequence from the q[] array + */ +double get_subseq_F(int i, int j); + +/** + * \brief Get the centroid structure of the ensemble + * + * This function is a threadsafe replacement for \ref centroid() with a 'plist' input + * + * The centroid is the structure with the minimal average distance to all other structures + * \n \f$ = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij} \f$ \n + * Thus, the centroid is simply the structure containing all pairs with \f$p_ij>0.5\f$ + * The distance of the centroid to the ensemble is written to the memory adressed by \a dist. + * + * \ingroup centroid_fold + * \param[in] length The length of the sequence + * \param[out] dist A pointer to the distance variable where the centroid distance will be written to + * \param[in] pl A pair list containing base pair probability information about the ensemble + * \return The centroid structure of the ensemble in dot-bracket notation + */ +char *get_centroid_struct_pl(int length, + double *dist, + plist *pl); + +/** + * \brief Get the centroid structure of the ensemble + * + * This function is a threadsafe replacement for \ref centroid() with a probability array input + * + * The centroid is the structure with the minimal average distance to all other structures + * \n \f$ = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij} \f$ \n + * Thus, the centroid is simply the structure containing all pairs with \f$p_ij>0.5\f$ + * The distance of the centroid to the ensemble is written to the memory adressed by \a dist. + * + * \ingroup centroid_fold + * \param[in] length The length of the sequence + * \param[out] dist A pointer to the distance variable where the centroid distance will be written to + * \param[in] pr A upper triangular matrix containing base pair probabilities (access via iindx \ref get_iindx() ) + * \return The centroid structure of the ensemble in dot-bracket notation + */ +char *get_centroid_struct_pr(int length, + double *dist, + FLT_OR_DBL *pr); + +/** + * \brief Get the mean base pair distance of the last partition function computation + * + * \note To ensure thread-safety, use the function mean_bp_distance_pr() instead! + * + * \ingroup pf_fold + * + * \see mean_bp_distance_pr() + * + * \param length + * \return mean base pair distance in thermodynamic ensemble + */ +double mean_bp_distance(int length); + +/** + * \brief Get the mean base pair distance in the thermodynamic ensemble + * + * This is a threadsafe implementation of \ref mean_bp_dist() ! + * + * \f$ = \sum_{a,b} p_a p_b d(S_a,S_b)\f$\n + * this can be computed from the pair probs \f$p_ij\f$ as\n + * \f$ = \sum_{ij} p_{ij}(1-p_{ij})\f$ + * + * \note This function is threadsafe + * + * \ingroup pf_fold + * + * \param length The length of the sequence + * \param pr The matrix containing the base pair probabilities + * \return The mean pair distance of the structure ensemble + */ +double mean_bp_distance_pr(int length, + FLT_OR_DBL *pr); + +/** + * \brief Create a dot-bracket like structure string from base pair probability matrix + */ +void bppm_to_structure(char *structure, + FLT_OR_DBL *pr, + unsigned int length); + +plist *stackProb(double cutoff); + +/** + * \brief Get a pseudo dot bracket notation for a given probability information + */ +char bppm_symbol(const float *x); + + +/* +################################################# +# DEPRECATED FUNCTIONS # +################################################# +*/ + +/** + * \brief Allocate space for pf_fold() + * + * \deprecated This function is obsolete and will be removed soon! + */ +DEPRECATED(void init_pf_fold(int length)); + +/** + * \deprecated This function is deprecated and should not be used anymore as it is not threadsafe! + * \see get_centroid_struct_pl(), get_centroid_struct_pr() + */ +DEPRECATED(char *centroid(int length, + double *dist)); /* mean pair distance of ensemble */ + +/** + * get the mean pair distance of ensemble + * + * \deprecated This function is not threadsafe and should not be used anymore. Use \ref mean_bp_distance() instead! + */ +DEPRECATED(double mean_bp_dist(int length)); + +/** + * \deprecated Use \ref exp_E_IntLoop() from loop_energies.h instead + */ +DEPRECATED(double expLoopEnergy(int u1, + int u2, + int type, + int type2, + short si1, + short sj1, + short sp1, + short sq1)); + +/** + * \deprecated Use exp_E_Hairpin() from loop_energies.h instead + */ +DEPRECATED(double expHairpinEnergy( int u, + int type, + short si1, + short sj1, + const char *string)); + +#endif diff --git a/src/part_func_co.h b/src/part_func_co.h new file mode 100755 index 0000000..8ef94c1 --- /dev/null +++ b/src/part_func_co.h @@ -0,0 +1,235 @@ +#ifndef __VIENNA_RNA_PACKAGE_PART_FUNC_CO_H__ +#define __VIENNA_RNA_PACKAGE_PART_FUNC_CO_H__ + +#include "data_structures.h" + +#ifdef __GNUC__ +#define DEPRECATED(func) func __attribute__ ((deprecated)) +#else +#define DEPRECATED(func) func +#endif + +/** + * \addtogroup pf_cofold + * \brief Partition Function Cofolding + * + * To simplify the implementation the partition function computation is done + * internally in a null model that does not include the duplex initiation + * energy, i.e. the entropic penalty for producing a dimer from two + * monomers). The resulting free energies and pair probabilities are initially + * relative to that null model. In a second step the free energies can be + * corrected to include the dimerization penalty, and the pair probabilities + * can be divided into the conditional pair probabilities given that a re + * dimer is formed or not formed. See \cite bernhart:2006 for further details. + * @{ + * \file part_func_co.h + * + * \brief Partition function for two RNA sequences + * + * As for folding one RNA molecule, this computes the partition function + * of all possible structures and the base pair probabilities. Uses the + * same global #pf_scale variable to avoid overflows. + * + * To simplify the implementation the partition function computation is done + * internally in a null model that does not include the duplex initiation + * energy, i.e. the entropic penalty for producing a dimer from two + * monomers). The resulting free energies and pair probabilities are initially + * relative to that null model. In a second step the free energies can be + * corrected to include the dimerization penalty, and the pair probabilities + * can be divided into the conditional pair probabilities given that a re + * dimer is formed or not formed. + * + * After computing the partition functions of all possible dimeres one + * can compute the probabilities of base pairs, the concentrations out of + * start concentrations and sofar and soaway. + * + * Dimer formation is inherently concentration dependent. Given the free + * energies of the monomers A and B and dimers AB, AA, and BB one can compute + * the equilibrium concentrations, given input concentrations of A and B, see + * e.g. Dimitrov & Zuker (2004) + */ + +/** + * \brief Toggles no intrabp in 2nd mol + */ +extern int mirnatog; + +/** + * \brief Free energies of the two monomers + */ +extern double F_monomer[2]; + +/** + * \brief Calculate partition function and base pair probabilities + * + * This is the cofold partition function folding. The second molecule starts + * at the #cut_point nucleotide. + * + * \note OpenMP: Since this function relies on the global parameters + * #do_backtrack, #dangles, #temperature and #pf_scale it is not + * threadsafe according to concurrent changes in these variables! + * Use co_pf_fold_par() instead to circumvent this issue. + * + * \see co_pf_fold_par() + * + * \param sequence Concatenated RNA sequences + * \param structure Will hold the structure or constraints + * \return cofoldF structure containing a set of energies needed for + * concentration computations. + */ +cofoldF co_pf_fold( char *sequence, + char *structure); + +/** + * \brief Calculate partition function and base pair probabilities + * + * This is the cofold partition function folding. The second molecule starts + * at the #cut_point nucleotide. + * + * \see get_boltzmann_factors(), co_pf_fold() + * + * \param sequence Concatenated RNA sequences + * \param structure Pointer to the structure constraint + * \param parameters Data structure containing the precalculated Boltzmann factors + * \param calculate_bppm Switch to turn Base pair probability calculations on/off (0==off) + * \param is_constrained Switch to indicate that a structure contraint is passed via the + * structure argument (0==off) + * \return cofoldF structure containing a set of energies needed for + * concentration computations. + */ +cofoldF co_pf_fold_par( char *sequence, + char *structure, + pf_paramT *parameters, + int calculate_bppm, + int is_constrained); + +/** + * \brief Get a pointer to the base pair probability array + * + * Accessing the base pair probabilities for a pair (i,j) is achieved by + * \verbatim FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; \endverbatim + * + * \see get_iindx() + * \return A pointer to the base pair probability array + */ +FLT_OR_DBL *export_co_bppm(void); + +/** + * \brief Free the memory occupied by co_pf_fold() + */ +void free_co_pf_arrays(void); + +/** + * \brief Recalculate energy parameters + * + * This function recalculates all energy parameters given + * the current model settings. + * + * \note This function relies on the global variables #pf_scale, #dangles and + * #temperature. Thus it might not be threadsafe in certain situations. + * Use update_co_pf_params_par() instead. + * + * \see get_boltzmann_factors(), update_co_pf_params_par() + * + * \param length Length of the current RNA sequence + */ +void update_co_pf_params(int length); + +/** + * \brief Recalculate energy parameters + * + * This function recalculates all energy parameters given + * the current model settings. + * It's second argument can either be NULL or a data structure + * containing the precomputed Boltzmann factors. In the first + * scenario, the necessary data structure will be created automatically + * according to the current global model settings, i.e. this + * mode might not be threadsafe. + * However, if the provided data structure is not NULL, threadsafety + * for the model parameters #dangles, #pf_scale and #temperature is regained, since their + * values are taken from this data structure during subsequent calculations. + * + * \see get_boltzmann_factors(), update_co_pf_params() + * + * \param length Length of the current RNA sequence + * \param parameters data structure containing the precomputed Boltzmann factors + */ +void update_co_pf_params_par(int length, + pf_paramT *parameters); + +/** + * \brief Compute Boltzmann probabilities of dimerization without homodimers + * + * Given the pair probabilities and free energies (in the null model) for a + * dimer AB and the two constituent monomers A and B, compute the conditional pair + * probabilities given that a dimer AB actually forms. + * Null model pair probabilities are given as a list as produced by + * assign_plist_from_pr(), the dimer probabilities 'prAB' are modified in place. + * + * \param FAB free energy of dimer AB + * \param FEA free energy of monomer A + * \param FEB free energy of monomer B + * \param prAB pair probabilities for dimer + * \param prA pair probabilities monomer + * \param prB pair probabilities monomer + * \param Alength Length of molecule A + */ +void compute_probabilities(double FAB, + double FEA, + double FEB, + struct plist *prAB, + struct plist *prA, + struct plist *prB, + int Alength); + +/** + * \brief Given two start monomer concentrations a and b, compute the + * concentrations in thermodynamic equilibrium of all dimers and the monomers. + * + * This function takes an array 'startconc' of input concentrations with alternating + * entries for the initial concentrations of molecules A and B (terminated by + * two zeroes), then computes the resulting equilibrium concentrations + * from the free energies for the dimers. Dimer free energies should be the + * dimer-only free energies, i.e. the FcAB entries from the #cofoldF struct. + * + * \param FEAB Free energy of AB dimer (FcAB entry) + * \param FEAA Free energy of AA dimer (FcAB entry) + * \param FEBB Free energy of BB dimer (FcAB entry) + * \param FEA Free energy of monomer A + * \param FEB Free energy of monomer B + * \param startconc List of start concentrations [a0],[b0],[a1],[b1],...,[an][bn],[0],[0] + * \return ConcEnt array containing the equilibrium energies and start concentrations + */ +ConcEnt *get_concentrations(double FEAB, + double FEAA, + double FEBB, + double FEA, + double FEB, + double *startconc); + + +/** + * @} + */ + +/* +################################################# +# DEPRECATED FUNCTIONS # +################################################# +*/ + +/** + * DO NOT USE THIS FUNCTION ANYMORE + * \deprecated{ This function is deprecated and will be removed soon!} + * use \ref assign_plist_from_pr() instead! + */ +DEPRECATED(plist *get_plist( struct plist *pl, + int length, + double cut_off)); +/** + * DO NOT USE THIS FUNCTION ANYMORE + * \deprecated{ This function is deprecated and will be removed soon!} + */ +DEPRECATED(void init_co_pf_fold(int length)); + +#endif diff --git a/src/profile.cpp b/src/profile.cpp new file mode 100644 index 0000000..bf7b7b4 --- /dev/null +++ b/src/profile.cpp @@ -0,0 +1,245 @@ +/* + * Profile.cpp + * + * Created on: Dec 18, 2016 + * Author: Amir Bayegan + */ + +#include "profile.h" + +Profile::Profile(const vector &pr1, + const vector &i1, + const vector > &hh1, vector< vector > coordinates, double b) { + p = pr1; + n = checkLength(); + m = p.size(); + ids= i1; + h = hh1; + computePSSM(); + h_sum = computeSumOfHeights(); + positions = coordinates; + bp=b; + + //checkPositions(); +} + +Profile::Profile() { + +} +Profile::~Profile() { + +} +Profile::Profile(const Profile & that){ + p = that.p; + n=that.n; + m = that.m; + ids = that.ids; + h=that.h; + pssm=that.pssm; + h_sum = that.h_sum; + positions = that.positions; + bp = that.bp; +} + +//Profile::Profile& operator=(const Profile &){ +// +//} + +void Profile::setLength(int nn){ + n=nn; +} + +int Profile::getLength(){ + return n; +} + +double Profile::getBp(){ + return bp; +} + +int Profile::getNumberOfSeqs(){ + return m; +} + +vector Profile::getSeqs(){ + return p; +} + +vector > Profile::getHeights(){ + return h; +} + +vector Profile::getIds(){ + return ids; +} + +vector< vector > Profile::getPSSM(){ + return pssm; +} + +void Profile::checkPositions(){ + int start,stop; + for (int i = 0; i > Profile::getPositions(){ + return positions; +} +void Profile::computePSSM(){ + int n = p[0].length(); + int m = p.size(); + float suma,sumc,sumg,sumu,sumgap; + + vector a,c,g,u,gap; + //printProfile("fasta"); + + for (int j = 0; j < n; ++j) { + suma=0,sumc=0,sumg=0,sumu=0,sumgap=0; + for (int i = 0; i < m; ++i) { + if (p[i][j]=='A') { + suma+=1; + } else if (p[i][j]=='C'){ + sumc+=1; + } else if (p[i][j]=='G'){ + sumg+=1; + } else if (p[i][j]=='U'){ + sumu+=1; + }else if (p[i][j]=='-'){ + sumgap+=1; + } + } + a.push_back(suma/m); + c.push_back(sumc/m); + g.push_back(sumg/m); + u.push_back(sumu/m); + gap.push_back(sumgap/m); + } + pssm.push_back(a); + pssm.push_back(c); + pssm.push_back(g); + pssm.push_back(u); + pssm.push_back(gap); + //print2Dvec(pssm); +} + +vector Profile::getSumOfHeights(){ + return h_sum; +} +vector Profile::computeSumOfHeights(){ + int n1 = h[0].size(); + int m1 = h.size(); + float sum; + vector h_sum(n,0); + + if (n!=n1 || m!=m1){ + reportErr("error in the heights of profiles!\n"); + } + + for (int j = 0; j < n; ++j) { + sum=0; + for (int i = 0; i < m; ++i) { + sum+=h[i][j]; + } + h_sum[j] =sum/m; + } + return h_sum; +} + +void Profile::reverseProfile(){ + /*positions remains untouched */ + int i,j; + for ( i = 0; i < m; ++i) { + reverse(p[i].begin(), p[i].end()); + reverse(h[i].begin(), h[i].end()); + } + for (i = 0; i < 5; ++i) { + reverse(pssm[i].begin(),pssm[i].end()); + } + reverse(h_sum.begin(),h_sum.end()); +} + + +void Profile::printProfile(string format){ + char tmp1[2000]; + int gapnum; + string tmpstr; + int i,j; + vector offset(m); + for(i=0;i0){ + for(i=0;i%s\n",ids[i].c_str() ); + j=c; + int offset1=0; + int start=0; + while(j>0){ + sprintf(outtxt+strlen(outtxt),"%s\n",p[i].substr(start,LINLEN).c_str()); + start+=LINLEN; + j--; + } + if(d>0){ + sprintf(outtxt+strlen(outtxt),"%s\n",p[i].substr(start,d).c_str()); + } + } + } +} diff --git a/src/profile.h b/src/profile.h new file mode 100644 index 0000000..f70a087 --- /dev/null +++ b/src/profile.h @@ -0,0 +1,60 @@ +/* + * Profile.h + * + * Created on: Dec 18, 2016 + * Author: Amir Bayegan + * + * Class contains a profile of aligned sequences. + * All the sequences in the profile must have the same length. + * This is used in ProfileAligner to build multiple or pairwise alignments. + */ + +#ifndef PROFILE_H_ +#define PROFILE_H_ + +#include +#include "aux.h" + +using namespace std; + + +class Profile { +public: + Profile(const vector &, + const vector &, + const vector > &, vector< vector >, double); + virtual ~Profile(); + Profile(); + Profile(const Profile &); + //Profile& operator=(const Profile &); + int getLength(); + void setLength(int); + int getNumberOfSeqs(); + vector getSeqs(); + vector > getHeights(); + vector getIds(); + vector< vector > getPSSM(); + vector > getPositions(); + void reverseProfile(); + vector computeSumOfHeights(); + vector getSumOfHeights(); + void printProfile(string); + double getBp(); + vector< vector > pssm;/*5 x m vector*/ + +private: + vector p; /*sequences*/ + vector > h; /*for each sequence there is an row vector of heights*/ + //vector< vector > pssm;/*5 x m vector*/ + vector h_sum; + int n; /*length of the alignments in the profiles*/ + int m; /*number of sequences in each profile*/ + double bp; /*average base pairing probability of sequences in the profile*/ + vector ids; /*sequence ids in the same order as sequences*/ + vector > positions;/*m by 2 vector of 0-indexed (start,stop) positions for each seq*/ + int checkLength(); + void checkPositions(); + void computePSSM(); +}; + +#endif /* PROFILE_H_ */ diff --git a/src/profile_aligner.cpp b/src/profile_aligner.cpp new file mode 100644 index 0000000..b405795 --- /dev/null +++ b/src/profile_aligner.cpp @@ -0,0 +1,553 @@ +/* + * ProfileAligner.cpp + * + * Created on: Dec 18, 2016 + * Author: Amir Bayegan + */ + +#include "profile_aligner.h" +#include +ProfileAligner::~ProfileAligner() { +} + +ProfileAligner::ProfileAligner(const Profile &pr1, const Profile &pr2, const Arguments & args, double shift, double mul) { + + p1 = pr1; + p2 = pr2; + len_aln=0; + aln_start[0]=0;aln_start[1]=0; + aln_stop[0]=p1.getLength();aln_stop[1]=p2.getLength(); + + /* alignment params*/ + max_score=-INF; + gap_init = args.gap_init; + gap_ext = args.gap_ext; + gap_init_str = args.gap_init_str; + gap_ext_str = args.gap_ext_str; + str_weight = args.str_weight; + //cut_off = percentile; + aln_type = args.aln_type; + calc_prob=false; + for (int i=0;i<=4;i++){ + for (int j=0;j<=4;j++){ + if (i!=4 && j!=4) { + seq_similarity[i][j]=args.subMat[i][j]; + } else if (i==4 or j==4) { + seq_similarity[i][j]=args.gap_ext; /* in computing SPS sim(X,'-')=Beta where X in{A,C,G,U}.*/ + } else{ + seq_similarity[i][j] =0; /* sim('-','-')=0 */ + } + } + } + + weighted_gap_init = (1-str_weight)*gap_init + str_weight*(gap_init_str); + weighted_gap_ext = (1-str_weight)*gap_ext + str_weight*(gap_ext_str); + + /*auxiliary matrices*/ + vector< vector > tmp0(p1.getLength()+1, vector(p2.getLength()+1,0)); + scoreMatrix_p = tmp0; + scoreMatrix_q = tmp0; + scoreMatrix_r = tmp0; + vector< vector > tmp1(p1.getLength()+1, vector(p2.getLength()+1,'N')); + pathMatrix_p =tmp1; + pathMatrix_q =tmp1; + pathMatrix_r =tmp1; + mult_seq=mul; shift_str=shift; + //similarity = buildSimilarityMatrix(); +// printf("*********similarity matrix***********"); +// printMatrix1(similarity,p1.getLength(),p2.getLength()); +// for (int i=0;i s1(p1.getNumberOfSeqs()+p2.getNumberOfSeqs()); + vector > h1(p1.getNumberOfSeqs()+p2.getNumberOfSeqs()); + max_score = max(scoreMatrix_p[n1][n2], + scoreMatrix_q[n1][n2], + scoreMatrix_r[n1][n2], + & matrix); + int x=n1; + int y = n2; + while(x>0 || y>0){ +// printf("%u,%u,%c\n",x,y,matrix); + if(matrix=='R'){ + extendProfile(s1,h1,x-1,y-1,0); + matrix = pathMatrix_r[x][y]; + x-=1;y-=1; + } + else if(matrix=='P'){ + extendProfile(s1,h1,x-1,y,2); + matrix = pathMatrix_p[x][y]; + x-=1; + } + else if(matrix=='Q'){ + extendProfile(s1,h1,x,y-1,1); + matrix = pathMatrix_q[x][y]; + y-=1; + } + } + vector alnids = mergeVectors(p1.getIds(),p2.getIds()); + vector > pos = computeAlignmentPositions(); + Profile alnp(s1,alnids,h1,pos,(p1.getBp()+p2.getBp())/2.0); + p = alnp; + len_aln=p.getLength(); + p.reverseProfile(); + + +} + + + + + +void ProfileAligner::buildSmithWatermanScoreMatrix(){ + //-----------initialize matrices + int n1 = p1.getLength(); + int n2 = p2.getLength(); + double sim; + scoreMatrix_p[0][0]=0; + scoreMatrix_q[0][0]=0; + scoreMatrix_r[0][0]=0; + for(int i=1;i<=n1;i++){ + scoreMatrix_p[i][0]= 0; + scoreMatrix_q[i][0]= 0; + scoreMatrix_r[i][0]= 0; + pathMatrix_p[i][0]='P'; + pathMatrix_q[i][0]='N'; //N is not used + pathMatrix_r[i][0]='N'; + } + for(int i=1;i<=n2;i++){ + scoreMatrix_p[0][i]= 0; + scoreMatrix_q[0][i]= 0; + scoreMatrix_r[0][i]= 0; + pathMatrix_q[0][i]='Q'; + pathMatrix_p[0][i]='N'; + pathMatrix_r[0][i]='N'; + } + + //------Fill the matrices + char ptr; + double maxv; + double simij; + for(int i=0;i s1(p1.getNumberOfSeqs()+p2.getNumberOfSeqs()); + vector > h1(p1.getNumberOfSeqs()+p2.getNumberOfSeqs()); + char matrix; + int x,y,stop1,stop2; + double score; + max_score=0; + + for (int i=1; i<=n1;i++){ + for(int j=1;j<=n2;j++){ + if(scoreMatrix_p[i][j] > max_score){ + max_score = scoreMatrix_p[i][j]; + x=i;y=j; + matrix='P'; + } + if (scoreMatrix_q[i][j] > max_score){ + max_score = scoreMatrix_q[i][j]; + x=i;y=j; + matrix='Q'; + } + if (scoreMatrix_r[i][j] > max_score){ + max_score = scoreMatrix_r[i][j]; + x=i;y=j; + matrix='R'; + } + } + } + aln_stop[0]=x;aln_stop[1]=y; + score = max_score; + + while(score>0){ + if(matrix=='R'){ + extendProfile(s1,h1,x-1,y-1,0); + matrix = pathMatrix_r[x][y]; + x-=1;y-=1; + } + else if(matrix=='P'){ + extendProfile(s1,h1,x-1,y,2); + matrix = pathMatrix_p[x][y]; + x-=1; + } + else if(matrix=='Q'){ + extendProfile(s1,h1,x,y-1,1); + matrix = pathMatrix_q[x][y]; + y-=1; + } + if(matrix=='P'){ + score=scoreMatrix_p[x][y]; + } + else if(matrix=='Q'){ + score = scoreMatrix_q[x][y]; + } + else if(matrix=='R'){ + score = scoreMatrix_r[x][y]; + } + } + aln_start[0]=x;aln_start[1]=y; + vector alnids = mergeVectors(p1.getIds(),p2.getIds()); + vector > pos = computeAlignmentPositions(); + Profile alnp(s1,alnids,h1,pos,(p1.getBp()+p2.getBp())/2.0); + p = alnp; + len_aln=p.getLength(); + p.reverseProfile(); +} + +float ProfileAligner::gap(int k){ + if (k<=0) + return 0; + else + return (1-str_weight)*(gap_init+gap_ext*(k-1)) + str_weight*(gap_init_str+gap_ext_str*(k-1) + (shift_str*k)/2.0); +} + +/*compute the value based on the given percentile +*to be used as MAX to convert distance of heights +to a measure of similarity in structural alignment.*/ +double ProfileAligner::computeMaxHeight(){ + double max1=-INF,min1=INF,max2=-INF,min2=INF; + for (int i = 0; i < p1.getNumberOfSeqs(); ++i) { + for (int j = 0; j < p1.getLength(); ++j) { + if (p1.getHeights()[i][j]>max1) { + max1=p1.getHeights()[i][j]; + } + if (p1.getHeights()[i][j]max2) { + max2=p2.getHeights()[i][j]; + } + if (p2.getHeights()[i][j] &s1,vector > &h1 ,int x, int y, int type){ + int i; + int m1 = p1.getNumberOfSeqs(); + int m2 = p2.getNumberOfSeqs(); + + /*-------------extend p and h----------*/ + if(type==0){ + for (i = 0; i < m1+m2; ++i) { + if(i > pssm1=p1.getPSSM(); + vector > pssm2=p2.getPSSM(); + for (int nuc0 = 0; nuc0 < 4; ++nuc0) { + for (int nuc1 = 0; nuc1 < 4; ++nuc1) { + sps += pssm1[nuc0][i]*pssm2[nuc1][j]*seq_similarity[nuc0][nuc1]; + } + + } + return sps; +} + +void ProfileAligner::computeQuality(){ + if(calc_prob){ + reportErr("partition function and probabilities not implemented yet!"); + } + else{ + for (int i=0;i > ProfileAligner::mergePositions(vector > v1,vector > v2){ + vector > v; + v.insert( v.end(), v1.begin(), v1.end() ); + v.insert( v.end(), v2.begin(), v2.end() ); + return v; +} + +vector > ProfileAligner::computeAlignmentPositions(){ + int i; + int m1 = p1.getNumberOfSeqs(); + int m2 = p2.getNumberOfSeqs(); + vector > v(m1+m2,vector(2,0)); + vector > pos1 = p1.getPositions(); + vector > pos2 = p2.getPositions(); + if(aln_type=='g'){ + v = mergePositions(pos1,pos2); + } + else{ + for (i = 0; i +#include +#include "aux.h" +#include "profile.h" +using namespace std; + +class ProfileAligner { +public: + ProfileAligner(const Profile &pr1, const Profile &pr2, const Arguments & args, double shift, double mul); + void printAlignment(string); + void computeQuality(); + Profile align(); + char getType(); + int getLength(); + int* getStart(); + int* getStop(); + double getScore(); + ProfileAligner(); + virtual ~ProfileAligner(); +private: + char aln_type; + Profile p1; + Profile p2; + Profile p; /*profile after alignment*/ + int aln_start[2]; + int aln_stop[2]; + int len_aln; + float gap_init; + float gap_ext; + float gap_init_str; + float gap_ext_str; + float weighted_gap_init; + float weighted_gap_ext; + float str_weight; + double mult_seq, shift_str; + int cut_off; + vector > scoreMatrix_p; + vector > scoreMatrix_q; + vector > scoreMatrix_r; + vector > pathMatrix_p; + vector > pathMatrix_q; + vector > pathMatrix_r; + const char * sub_mat_name; + float seq_similarity[5][5]; + //double ** similarity; + double max_score; + string quality; + float gap(int); + bool calc_prob; + + void buildNeedlemanWunschScoreMatrix(); + void backtrackNeedlemanWunsch(); + void buildSmithWatermanScoreMatrix(); + void backtrackSmithWaterman(); + double computeMaxHeight(); + double ** buildSimilarityMatrix(); + double similarity(int i,int j); + /*extends all sequences of the profile alignment by one character */ + void extendProfile(vector &, vector > &, int , int , int ); + /*reverse every sequence in the profile--move this to profile class*/ + void reverseProfile(); + double getSumOfPairsScore(int ,int ); + + /*keeps track of the alignment positions for every sequence in profiles(important for local alignment)*/ + vector > computeAlignmentPositions(); + vector > mergePositions(vector > ,vector >); + +}; + +#endif /* ENERGY_PARAMS_PROFILEALIGNER_H_ */ diff --git a/src/read_epars.h b/src/read_epars.h new file mode 100644 index 0000000..cadde7d --- /dev/null +++ b/src/read_epars.h @@ -0,0 +1,57 @@ +#ifndef __VIENNA_RNA_PACKAGE_READ_EPARS_H__ +#define __VIENNA_RNA_PACKAGE_READ_EPARS_H__ + +/** + * \addtogroup energy_parameters_rw + * \brief Read and Write energy parameter sets from and to text files + * + * A default set of parameters, identical to the one described in + * \cite mathews:2004 and \cite turner:2010, is compiled into the library. + * + * @{ + * \file read_epars.h + * + */ + +/** + * \brief + * + */ +enum parset { + UNKNOWN= -1, QUIT, + S, S_H, HP, HP_H, B, B_H, IL, IL_H, MMH, MMH_H, MMI, MMI_H, + MMI1N, MMI1N_H, MMI23, MMI23_H, MMM, MMM_H, MME, MME_H, D5, D5_H, D3, D3_H, + INT11, INT11_H, INT21, INT21_H, INT22, INT22_H, ML, TL, + TRI, HEX, NIN, MISC}; + +/** + * \brief Read energy parameters from a file + * + * \param fname The path to the file containing the energy parameters + */ +void read_parameter_file(const char fname[]); + +/** + * \brief Write energy parameters to a file + * + * \param fname A filename (path) for the file where the current energy parameters will be written to + */ +void write_parameter_file(const char fname[]); + +/** + * \brief + * + */ +enum parset gettype(const char *ident); + +/** + * \brief + * + */ +char *settype(enum parset s); + +/** + * @} + */ + +#endif diff --git a/src/stats.cpp b/src/stats.cpp new file mode 100644 index 0000000..c63558b --- /dev/null +++ b/src/stats.cpp @@ -0,0 +1,294 @@ +#include "stats.h" + +double computeEvalue_EVD(double x, double lambda, double mu ){ + return exp(-1.0 * lambda * (x - mu)); +} + +//This function is adapted from John D. Cook +double cdf_normal(double x){ + //A&S refers to Handbook of Mathematical Functions by Abramowitz and Stegun + // constants + double a1 = 0.254829592; + double a2 = -0.284496736; + double a3 = 1.421413741; + double a4 = -1.453152027; + double a5 = 1.061405429; + double p = 0.3275911; + + // Save the sign of x + int sign = 1; + if (x < 0) + sign = -1; + x = fabs(x)/sqrt(2.0); + + // A&S formula 7.1.26 + double t = 1.0/(1.0 + p*x); + double y = 1.0 - (((((a5*t + a4)*t) + a3)*t + a2)*t + a1)*t*exp(-x*x); + + return 0.5*(1.0 + sign*y); +} + +double computePvalueNormal(double x, double sigma, double mu){ + double z=(x-mu)/sigma; + return 1.0 - cdf_normal(z); +} + +//EML = 0.1764 + 0.7991 * E_KA +double KAevalueRegressionTransform(double KA){ + //return 0.1764 + 0.7991 * KA; + return 0.7991 * KA; +} + +double computeEvalue(double x, double lambda, double K, int N){ + return K*N*exp(-1.0*lambda*x); +} + +double computeK(double EVDlambda, double EVDmu,int n){ + return exp(EVDlambda*EVDmu)/n; +} + +double comuteMu(double lambda, double K, int N){ + return log(K*N)/lambda; +} + +double Eval2Pval(double e){ + return 1-exp(-e); +} + +double Pval2Eval(double p){ + return -log(1-p); +} + +double computeVectorMean(vector vec){ + double sum=0.0; + for (int i=0;i vec, double mu){ + double sum=0.0; + for (int i=0;i &npr1, const vector &npr2 , score_prob &sc_pr, const float subMat[4][4] ){ + const char *nuc="ACGU"; + int i,j; + for (i=0;i<4;i++){ + for (j=0;j<4;j++){ + if (i!=j){ + sc_pr.scmap[subMat[char2num(nuc[i])][char2num(nuc[j])]]= npr1[char2num(nuc[i])]*npr2[char2num(nuc[j])] + npr1[char2num(nuc[j])]*npr2[char2num(nuc[i])]; + } + else{ + sc_pr.scmap[subMat[char2num(nuc[i])][char2num(nuc[i])]]=npr1[char2num(nuc[i])]*npr2[char2num(nuc[i])]; + } + } + } + sc_pr.checkProb(); +} + + +void karlinStats(const vector &npr1,double **bppr1, int n1, const vector &npr2, double **bppr2, int n2, const float subMat[4][4],float gamma,double &K, double &lambda){ + //printf("Beginning of karlinStats\n"); + double bpprob1,bpprob2; + score_prob str_prob,seq_prob,comb_pr; + double mu_seq=0.0,std_seq=0.0,mu_str=0.0,std_str=0.0; + double mult_seq=1.0,shift_str=1.0; + int i,j; + mapit str_it,seq_it; + double seq_sc,seq_pr,str_sc,str_pr; + + bpprob1 = basePairProbability(bppr1,n1); + bpprob2 = basePairProbability(bppr2,n2); + //printf("BP probs: %f,%f\n",bpprob1,bpprob2); + absDiffBpProbability(bpprob1,bpprob2,str_prob); + //str_prob.print(); + nucMutationProb(npr1,npr2,seq_prob,subMat); + //seq_prob.print(); + mu_str = str_prob.expectedValue(); + std_str = str_prob.standard_deviation(mu_str); + + mu_seq = seq_prob.expectedValue(); + std_seq = seq_prob.standard_deviation(mu_seq); + + //printf("museq=%f;stdseq=%f\n",mu_seq,std_seq); + //printf("mustr=%f;stdstr=%f\n",mu_str,std_str); + if (!equal(std_seq,0.0) and !equal(std_str,0.0)){ + mult_seq = std_str/std_seq; + } + shift_str = mult_seq*mu_seq - mu_str; + //printf("shift_str=%f,mult_seq=%f\n",shift_str,mult_seq); + for ( seq_it = seq_prob.scmap.begin(); seq_it != seq_prob.scmap.end(); ++seq_it ){ + seq_sc=seq_it->first;seq_pr=seq_it->second; + for ( str_it = str_prob.scmap.begin(); str_it != str_prob.scmap.end(); ++str_it ){ + str_sc=str_it->first;str_pr=str_it->second; + if(gamma<0){ + gamma = (bpprob1+bpprob2)/2.0; + } + comb_pr.scmap[gamma*(str_sc+shift_str) + (1.0-gamma)*(seq_sc*mult_seq)]= seq_pr*str_pr; + } + } + //comb_pr.checkProb(); + //comb_pr.print(); + //printf("expScore:%f\n",comb_pr.expectedValue()); + karlin_altschul(comb_pr,K,lambda); +} + +void computeStats_bin_gc( Arguments & args, vector & gc_vec, vector > & gc_mu_lam_vec,const char distr){ + int i; + + float pa,pc,pg,pu; + + //int randlen = 2*qlen; + double lambda,mu,K; + float gc_max,gc_min,gc,gc_low,gc_high; + int qlen = args.seqs[0].size(); + int randlen = args.window_size; + vector topscore_vec; + vector row; + char fname[100]; + if (!args.qsearch) + randlen=args.seqs[1].length(); + //variables for computing the expected heights + double MFEq,ensEngq,MFEr,ensEngr; + double ** bpprq = allocate2DdoubleArray(qlen,qlen+1); + double ** bpprref = allocate2DdoubleArray(randlen,randlen+1); + char * sq = new char[qlen+1]; + char * sr = new char[randlen+1]; + char * mfeStrq = new char[qlen+1]; + char * mfeStrr = new char[randlen+1]; + char * randseq = new char[randlen+1]; + vector hq,hr; + + strcpy(sq,args.seqs[0].c_str()); + BasePairProbabilities(sq,qlen,&MFEq,mfeStrq,&ensEngq,args.argv0,bpprq); + //compute heights for the query sequence + if(args.modified_height){ + hq = expectedModifiedHeight(bpprq,qlen); + } + else{ + hq = expectedHeight(bpprq,qlen); + } + hq=heightDiff(hq); + sort(gc_vec.begin(),gc_vec.end()); + gc_min = gc_vec.front(); + gc_max = gc_vec.back(); + for (gc_low=gc_min;gc_low<=gc_max;gc_low+=args.gc_seg){ + gc_high = gc_low+ args.gc_seg; + if(gc_high>gc_max) + gc_high=gc_max; + gc = (gc_high + gc_low)/2.0; //take the middle point in each GC range + + pc = pg = 0.5 *gc; + pa = pu = 0.5 *(1-gc); + + row.clear(); + topscore_vec.clear(); + for(i=0 ; i < args.rnd_num; ++i){ //start sampling random RNAs + generateRandomRNA(randseq,randlen,pa,pc,pg,pu); + //fold the RNA and get heights + BasePairProbabilities(randseq,randlen,&MFEr,mfeStrr,&ensEngr,args.argv0,bpprref); + if(args.modified_height){ + hr = expectedModifiedHeight(bpprref,randlen); + } + else{ + hr = expectedHeight(bpprref,randlen); + } + hr = heightDiff(hr); + //perform the local alignment + Alignment aligner(args.seqs[0],randseq,hq,hr,bpprq,bpprref,args); + aligner.align(); + topscore_vec.push_back(aligner.getScore()); + //aligner.printAlignment(); + } + //write random scores to output + //sprintf(fname,"%s_%.2f_%d_random_scores",args.fasta_name.c_str(),gc,args.rnd_num); + //writeVec(fname,topscore_vec); + + if (distr=='N'){ + mu = computeVectorMean(topscore_vec); + lambda = computeVectorStd(topscore_vec,mu); + } + else if (distr=='E'){ + //fit scores to EVD distributions and get the parameters + EVD g(topscore_vec,true); + if (!g.fit()) reportErr("Error in max likelihood fit of scores to EVD distribution\n"); + lambda = g.getLambda(); + K = computeK(lambda,g.getMu(),randlen); + mu = comuteMu(lambda,K,randlen);//IMPORTANT: don't mix up the EVD mu with Karlin/Altschul mu. + } + row.push_back(gc_low);row.push_back(gc_high);row.push_back(mu);row.push_back(lambda); + gc_mu_lam_vec.push_back(row); + } + printStats( args.rnd_num, randlen, gc_mu_lam_vec); + free2DdoubleArray(bpprq,qlen); + free2DdoubleArray(bpprref,randlen); + delete [] sq; + delete [] sr; + delete [] mfeStrq; + delete [] mfeStrr; +} + + +//gc_vec: +void get_params_for_gc(float gc, vector > & gc_mu_lam_vec, double & lambda , double & mu ){ + for (int i = 0; i < gc_mu_lam_vec.size(); ++i){ + if(gc_mu_lam_vec[i][0]<= gc && gc < gc_mu_lam_vec[i][1]){ + mu = gc_mu_lam_vec[i][2]; + lambda = gc_mu_lam_vec[i][3]; + return; + } + if((gc-gc_mu_lam_vec[i][1])<0.00001){ //The last bin is inclusive for both beg and end + mu = gc_mu_lam_vec[i][2]; + lambda = gc_mu_lam_vec[i][3]; + return; + } + } + reportErr("Error in get_params_for_gc(). GC content not found!\n"); +} + +void printStats(int rnd_num, int randlen,vector > gc_mu_lam_vec){ + int n = gc_mu_lam_vec.size(); + printf("#Stats:\n"); + + printf("GC Bins: "); + for (int i=0; i +#include + +#include "aux.h" +#include "mountain_height.h" +#include "arguments.h" +#include "pair_align.h" +#include "evd.h" +#include "karlin_altschul.h" + + +void absDiffBpProbability(const double &bp1, const double &bp2, score_prob &sc_pr); +void nucMutationProb(const vector &npr1, const vector &npr2 , score_prob &sc_pr, const float mat[4][4]); +void karlinStats(const vector &npr1,double **bppr1, int n1, const vector &npr2, double **bppr2, int n2, const float subMat[4][4],float gamma,double &K, double &lambda); +void computeStats_bin_gc( Arguments & args, vector & gc_vec, vector > & gc_mu_lam_vec,const char dist); +double computeEvalue_EVD(double x, double lambda, double mu); +double computeEvalue(double x, double lambda, double K, int N); +double computeK(double lambda, double mu,int n); +double comuteMu(double lambda, double K, int N); +void get_params_for_gc(float gc, vector > & gc_mu_lam_vec, double & lambda , double & mu ); +void printStats(int RND_NUM, int randlen,vector > gc_mu_lam_vec); +double computeVectorMean(vector vec); +double computeVectorStd(vector vec, double mu); +double computePvalueNormal(double x, double sigma, double mu); +double cdf_normal(double x); +double Eval2Pval(double e); +double Pval2Eval(double p); +double KAevalueRegressionTransform(double KA); +#endif /* STATS_H_ */ diff --git a/src/utils.h b/src/utils.h new file mode 100644 index 0000000..68b66ce --- /dev/null +++ b/src/utils.h @@ -0,0 +1,615 @@ +#ifndef __VIENNA_RNA_PACKAGE_UTILS_H__ +#define __VIENNA_RNA_PACKAGE_UTILS_H__ + +/** + * \file utils.h + * \brief Various utility- and helper-functions used throughout the Vienna RNA package + */ + +/** + * Output flag of \ref get_input_line(): "An ERROR has occured, maybe EOF" + */ +#define VRNA_INPUT_ERROR 1U +/** + * Output flag of \ref get_input_line(): "the user requested quitting the program" + */ +#define VRNA_INPUT_QUIT 2U +/** + * Output flag of \ref get_input_line(): "something was read" + */ +#define VRNA_INPUT_MISC 4U + +/** Input/Output flag of \ref get_input_line():\n + * if used as input option this tells get_input_line() that the data to be read should comply + * with the FASTA format + * + * the function will return this flag if a fasta header was read + */ +#define VRNA_INPUT_FASTA_HEADER 8U + +/** Input flag for get_input_line():\n + * Tell get_input_line() that we assume to read a nucleotide sequence + * + */ +#define VRNA_INPUT_SEQUENCE 16U + +/** Input flag for get_input_line():\n + * Tell get_input_line() that we assume to read a structure constraint + * + */ +#define VRNA_INPUT_CONSTRAINT 32U + +/** + * Input switch for \ref get_input_line(): + * "do not trunkate the line by eliminating white spaces at end of line" + */ +#define VRNA_INPUT_NO_TRUNCATION 256U + +/** + * Input switch for read_record(): "do fill rest array" + */ +#define VRNA_INPUT_NO_REST 512U + +/** + * Input switch for read_record(): "never allow data to span more than one line" + */ +#define VRNA_INPUT_NO_SPAN 1024U + +/** + * Input switch for read_record(): "do not skip empty lines" + */ +#define VRNA_INPUT_NOSKIP_BLANK_LINES 2048U + +/** + * Output flag for read_record(): "read an empty line" + */ +#define VRNA_INPUT_BLANK_LINE 4096U + +/** + * Input switch for \ref get_input_line(): "do not skip comment lines" + */ +#define VRNA_INPUT_NOSKIP_COMMENTS 128U + +/** + * Output flag for read_record(): "read a comment" + */ +#define VRNA_INPUT_COMMENT 8192U + + + + +/** + * pipe sign '|' switch for structure constraints (paired with another base) + */ +#define VRNA_CONSTRAINT_PIPE 1U +/** + * dot '.' switch for structure constraints (no constraint at all) + */ +#define VRNA_CONSTRAINT_DOT 2U +/** + * 'x' switch for structure constraint (base must not pair) + */ +#define VRNA_CONSTRAINT_X 4U +/** + * angle brackets '<', '>' switch for structure constraint (paired downstream/upstream) + */ +#define VRNA_CONSTRAINT_ANG_BRACK 8U +/** + * round brackets '(',')' switch for structure constraint (base i pairs base j) + */ +#define VRNA_CONSTRAINT_RND_BRACK 16U +/** + * constraint may span over several lines + */ +#define VRNA_CONSTRAINT_MULTILINE 32U +/** + * do not print the header information line + */ +#define VRNA_CONSTRAINT_NO_HEADER 64U +/** + * placeholder for all constraining characters + */ +#define VRNA_CONSTRAINT_ALL 128U +/** + * '+' switch for structure constraint (base is involved in a gquad) + */ +#define VRNA_CONSTRAINT_G 256U + + + +/** + * Tell a function that an input is assumed to span several lines if used as input-option + * A function might also be returning this state telling that it has read data from + * multiple lines. + * + * \see extract_record_rest_structure(), read_record(), getConstraint() + * + */ +#define VRNA_OPTION_MULTILINE 32U + + +/** + * Get the minimum of two comparable values + */ +#define MIN2(A, B) ((A) < (B) ? (A) : (B)) +/** + * Get the maximum of two comparable values + */ +#define MAX2(A, B) ((A) > (B) ? (A) : (B)) +/** + * Get the minimum of three comparable values + */ +#define MIN3(A, B, C) (MIN2( (MIN2((A),(B))) ,(C))) +/** + * Get the maximum of three comparable values + */ +#define MAX3(A, B, C) (MAX2( (MAX2((A),(B))) ,(C))) + + +/** + * Stringify a macro after expansion + */ +#define XSTR(s) STR(s) +/** + * Stringify a macro argument + */ +#define STR(s) #s + +#ifndef FILENAME_MAX_LENGTH +/** + * \brief Maximum length of filenames that are generated by our programs + * + * This definition should be used throughout the complete ViennaRNA package + * wherever a static array holding filenames of output files is declared. + */ +#define FILENAME_MAX_LENGTH 80 +/** + * \brief Maximum length of id taken from fasta header for filename generation + * + * this has to be smaller than FILENAME_MAX_LENGTH since in most cases, + * some suffix will be appended to the ID + */ +#define FILENAME_ID_LENGTH 42 +#endif + + +#ifdef HAVE_CONFIG_H +#include +#ifndef HAVE_STRDUP +char *strdup(const char *s); +#endif +#endif +#ifdef WITH_DMALLOC +/* use dmalloc library to check for memory management bugs */ +#include "dmalloc.h" +#define space(S) calloc(1,(S)) +#else + +/** + * \brief Allocate space safely + * + * \param size The size of the memory to be allocated in bytes + * \return A pointer to the allocated memory + */ +/*@only@*/ /*@notnull@*/ +void *space(unsigned size) /*@ensures MaxSet(result) == (size-1);@*/; + +/** + * \brief Reallocate space safely + * + * \param p A pointer to the memory region to be reallocated + * \param size The size of the memory to be allocated in bytes + * \return A pointer to the newly allocated memory + */ +/*@only@*/ /*@notnull@*/ +void *xrealloc(/*@null@*/ /*@only@*/ /*@out@*/ /*@returned@*/ void *p, + unsigned size) /*@modifies *p @*/ /*@ensures MaxSet(result) == (size-1) @*/; +#endif + +/** + * \brief Die with an error message + * + * \see warn_user() + * \param message The error message to be printed before exiting with 'FAILURE' + */ +/*@exits@*/ +void nrerror(const char message[]); + +/** + * \brief Print a warning message + * + * Print a warning message to \e stderr + * + * \param message The warning message + */ +void warn_user(const char message[]); + +/** + * \brief Make random number seeds + */ +void init_rand(void); + +/** + * \brief Current 48 bit random number + * + * This variable is used by urn(). These should be set to some + * random number seeds before the first call to urn(). + * + * \see urn() + */ +extern unsigned short xsubi[3]; + +/** + * \brief get a random number from [0..1] + * + * \note Usually implemented by calling \e erand48(). + * \return A random number in range [0..1] + */ +double urn(void); + +/** + * \brief Generates a pseudo random integer in a specified range + * + * \param from The first number in range + * \param to The last number in range + * \return A pseudo random number in range [from, to] + */ +int int_urn(int from, int to); + +void filecopy(FILE *from, FILE *to); /* inefficient `cp' */ + +/** + * \brief Get a timestamp + * + * Returns a string containing the current date in the format + * \verbatim Fri Mar 19 21:10:57 1993\endverbatim + * + * \return A string containing the timestamp + */ +/*@observer@*/ +char *time_stamp(void); + +/** + * \brief Create a random string using characters from a specified symbol set + * + * \param l The length of the sequence + * \param symbols The symbol set + * \return A random string of length 'l' containing characters from the symbolset + */ +/*@only@*/ /*@notnull@*/ +char *random_string(int l, const char symbols[]); + +/** + * \brief Calculate hamming distance between two sequences + * + * Calculate the number of positions in which + * \param s1 The first sequence + * \param s2 The second sequence + * \return The hamming distance between s1 and s2 + */ +int hamming(const char *s1, const char *s2); + +/** + * \brief Calculate hamming distance between two sequences up to a specified length + * + * This function is similar to hamming() but instead of comparing both sequences + * up to their actual length only the first 'n' characters are taken into account + * \param s1 The first sequence + * \param s2 The second sequence + * \return The hamming distance between s1 and s2 + */ +int hamming_bound(const char *s1, const char *s2, int n); + +/** + * \brief Read a line of arbitrary length from a stream + * + * Returns a pointer to the resulting string. The necessary memory is + * allocated and should be released using \e free() when the string is + * no longer needed. + * + * \param fp A file pointer to the stream where the function should read from + * \return A pointer to the resulting string + */ +/*@only@*/ /*@null@*/ +char *get_line(FILE *fp); + +int skip_comment_lines(char **line); + +/** + * Retrieve a line from 'stdin' savely while skipping comment characters and + * other features + * This function returns the type of input it has read if recognized. + * An option argument allows to switch between different reading modes.\n + * Currently available options are:\n + * #VRNA_INPUT_NOPRINT_COMMENTS, #VRNA_INPUT_NOSKIP_COMMENTS, #VRNA_INPUT_NOELIM_WS_SUFFIX + * + * pass a collection of options as one value like this: + * \verbatim get_input_line(string, option_1 | option_2 | option_n) \endverbatim + * + * If the function recognizes the type of input, it will report it in the return + * value. It also reports if a user defined 'quit' command (@-sign on 'stdin') + * was given. Possible return values are:\n + * #VRNA_INPUT_FASTA_HEADER, #VRNA_INPUT_ERROR, #VRNA_INPUT_MISC, #VRNA_INPUT_QUIT + * + * \param string A pointer to the character array that contains the line read + * \param options A collection of options for switching the functions behavior + * \return A flag with information about what has been read + */ +unsigned int get_input_line(char **string, + unsigned int options); + +unsigned int get_multi_input_line(char **string, + unsigned int options); + +/** + * \brief Get a data record from stdin + * + * This function may be used to obtain complete datasets from stdin. A dataset is always + * defined to contain at least a sequence. If data on stdin starts with a fasta header, + * i.e. a line like + * \verbatim >some header info \endverbatim + * then read_record() will assume that the sequence that follows the header may span + * over several lines. To disable this behavior and to assign a single line to the argument + * 'sequence' one can pass VRNA_INPUT_NO_SPAN in the 'options' argument. + * If no fasta header is read in the beginning of a data block, a sequence must not span over + * multiple lines!\n + * Unless the options #VRNA_INPUT_NOSKIP_COMMENTS or #VRNA_INPUT_NOSKIP_BLANK_LINES are passed, + * a sequence may be interrupted by lines starting with a comment character or empty lines.\n + * A sequence is regarded as completely read if it was either assumed to not span over multiple + * lines, a secondary structure or structure constraint follows the sequence on the next line + * or a new header marks the beginning of a new sequence...\n + * All lines following the sequence (this includes comments) and not initiating a new dataset are + * available through the line-array 'rest'. Here one can usually find the structure constraint or + * other information belonging to the current dataset. Filling of 'rest' may be prevented by + * passing #VRNA_INPUT_NO_REST to the options argument.\n + * + * \note This function will exit any program with an error message if no sequence could be read! + * + * The main purpose of this function is to be able to easily parse blocks of data from stdin + * in the header of a loop where all calculations for the appropriate data is done inside the + * loop. The loop may be then left on certain return values, e.g.: + * \verbatim +char *id, *seq, **rest; +int i; +while(!(read_record(&id, &seq, &rest, 0) & (VRNA_INPUT_ERROR | VRNA_INPUT_QUIT))){ + if(id) printf("%s\n", id); + printf("%s\n", seq); + if(rest) + for(i=0;rest[i];i++) + printf("%s\n", rest[i]); +} \endverbatim + * + * In the example above, the while loop will be terminated when read_record() returns either an + * error or a user initiated quit request.\n + * As long as data is read from stdin, the id is printed if it is available for the current block + * of data. The sequence will be printed in any case and if some more lines belong to the current + * block of data each line will be printed as well. + * + * \note Do not forget to free the memory occupied by header, sequence and rest! + * + * \param header A pointer which will be set such that it points to the header of the record + * \param sequence A pointer which will be set such that it points to the sequence of the record + * \param rest A pointer which will be set such that it points to an array of lines which also belong to the record + * \param options Some options which may be passed to alter the behavior of the function, use 0 for no options + * \return A flag with information about what the function actually did read + */ +unsigned int read_record( char **header, + char **sequence, + char ***rest, + unsigned int options); + + +/* \brief Extract a dot-bracket structure string from (multiline)character array + * + * This function extracts a dot-bracket structure string from the 'rest' array as + * returned by read_record() and returns it. All occurences of comments within the + * 'lines' array will be skipped as long as they do not break the structure string. + * If no structure could be read, this function returns NULL. + * + * \see read_record() + * + * \param lines The (multiline) character array to be parsed + * \param length The assumed length of the dot-bracket string (passing a value < 1 results in no length limit) + * \param option Some options which may be passed to alter the behavior of the function, use 0 for no options + * \return The dot-bracket string read from lines or NULL + */ +char *extract_record_rest_structure(const char **lines, + unsigned int length, + unsigned int option); + +/** + * \brief Pack secondary secondary structure, 5:1 compression using base 3 encoding + * + * Returns a binary string encoding of the secondary structure using + * a 5:1 compression scheme. The string is NULL terminated and can + * therefore be used with standard string functions such as strcmp(). + * Useful for programs that need to keep many structures in memory. + * + * \param struc The secondary structure in dot-bracket notation + * \return The binary encoded structure + */ +char *pack_structure(const char *struc); + +/** + * \brief Unpack secondary structure previously packed with pack_structure() + * + * Translate a compressed binary string produced by pack_structure() back into + * the familiar dot-bracket notation. + * + * \param packed The binary encoded packed secondary structure + * \return The unpacked secondary structure in dot-bracket notation + */ +char *unpack_structure(const char *packed); + +/** + * \brief Create a pair table of a secondary structure + * + * Returns a newly allocated table, such that table[i]=j if (i.j) pair + * or 0 if i is unpaired, table[0] contains the length of the structure. + * + * \param structure The secondary structure in dot-bracket notation + * \return A pointer to the created pair_table + */ +short *make_pair_table(const char *structure); + +short *make_pair_table_pk(const char *structure); + +/** + * \brief Get an exact copy of a pair table + * + * \param pt The pair table to be copied + * \return A pointer to the copy of 'pt' + */ +short *copy_pair_table(const short *pt); + +/** +***Pair table for snoop align +*** +*** +**/ +short *alimake_pair_table(const char *structure); + +/** +*** returns a newly allocated table, such that: table[i]=j if (i.j) pair or +*** 0 if i is unpaired, table[0] contains the length of the structure. +*** The special pseudoknotted H/ACA-mRNA structure is taken into account. +**/ +short *make_pair_table_snoop(const char *structure); + +/** + * \brief Compute the "base pair" distance between two secondary structures s1 and s2. + * + * The sequences should have the same length. + * dist = number of base pairs in one structure but not in the other + * same as edit distance with open-pair close-pair as move-set + * + * \param str1 First structure in dot-bracket notation + * \param str2 Second structure in dot-bracket notation + * \return The base pair distance between str1 and str2 + */ + +int *make_loop_index_pt(short *pt); + + +int bp_distance(const char *str1, + const char *str2); + +/** + * \brief Print a line to \e stdout that asks for an input sequence + * + * There will also be a ruler (scale line) printed that helps orientation of the sequence positions + */ +void print_tty_input_seq(void); + +/** + * \brief Print a line with a user defined string and a ruler to stdout. + * + * (usually this is used to ask for user input) + * There will also be a ruler (scale line) printed that helps orientation of the sequence positions + * + * \param s A user defined string that will be printed to stdout + */ +void print_tty_input_seq_str(const char *s); + +/** + * \brief Print structure constraint characters to stdout + * (full constraint support) + * + */ +void print_tty_constraint_full(void); + +/** + * \brief Print structure constraint characters to stdout. + * (constraint support is specified by option parameter) + * + * Currently available options are:\n + * #VRNA_CONSTRAINT_PIPE (paired with another base)\n + * #VRNA_CONSTRAINT_DOT (no constraint at all)\n + * #VRNA_CONSTRAINT_X (base must not pair)\n + * #VRNA_CONSTRAINT_ANG_BRACK (paired downstream/upstream)\n + * #VRNA_CONSTRAINT_RND_BRACK (base i pairs base j)\n + * + * pass a collection of options as one value like this: + * \verbatim print_tty_constraint(option_1 | option_2 | option_n) \endverbatim + * + * \param option Option switch that tells which constraint help will be printed + */ +void print_tty_constraint(unsigned int option); + +/** + * \brief Convert a DNA input sequence to RNA alphabet + * + * This function substitudes T and t with U and u, respectively + * + * \param sequence The sequence to be converted + */ +void str_DNA2RNA(char *sequence); + +/** + * \brief Convert an input sequence to uppercase + * + * \param sequence The sequence to be converted + */ +void str_uppercase(char *sequence); + +/** + * \brief Get an index mapper array (iindx) for accessing the energy matrices, e.g. in partition function related functions. + * + * Access of a position "(i,j)" is then accomplished by using \verbatim (i,j) ~ iindx[i]-j \endverbatim + * This function is necessary as most of the two-dimensional energy matrices are actually one-dimensional arrays throughout + * the ViennaRNAPackage + * + * Consult the implemented code to find out about the mapping formula ;) + * + * \see get_indx() + * \param length The length of the RNA sequence + * \return The mapper array + */ +int *get_iindx(unsigned int length); + +/** + * \brief Get an index mapper array (indx) for accessing the energy matrices, e.g. in MFE related functions. + * + * Access of a position "(i,j)" is then accomplished by using \verbatim (i,j) ~ indx[j]+i \endverbatim + * This function is necessary as most of the two-dimensional energy matrices are actually one-dimensional arrays throughout + * the ViennaRNAPackage + * + * Consult the implemented code to find out about the mapping formula ;) + * + * \see get_iindx() + * \param length The length of the RNA sequence + * \return The mapper array + * + */ +int *get_indx(unsigned int length); + +void getConstraint( char **cstruc, + const char **lines, + unsigned int option); + +/** + * \brief Insert constraining pair types according to constraint structure string + * + * \see get_indx(), get_iindx() + * + * \param constraint The structure constraint string + * \param length The actual length of the sequence (constraint may be shorter) + * \param ptype A pointer to the basepair type array + * \param min_loop_size The minimal loop size (usually \ref TURN ) + * \param idx_type Define the access type for base pair type array (0 = indx, 1 = iindx) + */ +void constrain_ptypes(const char *constraint, + unsigned int length, + char *ptype, + int *BP, + int min_loop_size, + unsigned int idx_type); + +unsigned int *make_referenceBP_array(short *reference_pt, + unsigned int turn); + +unsigned int *compute_BPdifferences( short *pt1, + short *pt2, + unsigned int turn); + +#endif