earlier CCTCCTT prevents finding leader/D1

[phycologia]

Code worked and found boxb but couldn't find leader or D1--D1 has typical start and end sequences, so I think it may be because there is an earlier "CCTCCTT" which occurs in the sequence

accession number:
MT135015.1

[nlabrad]

@phycologia what are the flanking regions for this one?
I noticed a potential issue that would make it not find the start, but now I'm dealing with the ends not showing up. Can you confirm what the closing flanking region should be?

I find GACAA as a start (2 of them) and the matching end I have for that is '[AT]TGTC' which means either ATGTC or TTGTC, there is a ATGTC but 500 bases down so I don't think that's it. Am I missing one end for that?
@callmcgovern also check if this makes sense.

[phycologia]

@nlabrad D1 begins with GACCT and ends with AGGTC

[nlabrad]

Aha, I see it. And now I see what you mean. Maybe if there is more than one ITS starting pattern found we do something. Maybe if there is more than one and d1d1 is not found we try again, idk

[phycologia]

@nlabrad @callmcgovern have we ever come across a sequence that doesn't have "AGGGA" right at the beginning of the ITS region? if that's always present then what if the code searched for "CCTCCT[TA]" followed by "(however you would code '2 or 3 variable bases')" followed by "AGGGA"? what's the range of leader sequence lengths we've seen? I think I've found only 7 & 8, but if it's sometimes longer then I guess it'd need to be a wider range of # of bases between CCTCCT[TA] and AGGGA