diff --git a/src/padlock.h b/src/padlock.h
index 498f806..53062ec 100644
--- a/src/padlock.h
+++ b/src/padlock.h
@@ -401,9 +401,13 @@ namespace dicey
 	    ofile << gRegions[refIndex][i].strand << '\t';
 	    ofile << c.chrname[refIndex] << ':' << gRegions[refIndex][i].start + 1 << '-' << gRegions[refIndex][i].end + 1 << '\t';
 	    ofile << arm1 << '-' << arm2 << '\t';
-	    ofile << c.spacerleft << '\t' << c.anchor << '\t';
+	    if (c.spacerleft.size()) ofile << c.spacerleft << '\t';
+	    else ofile << "n.a." << '\t';
+	    if (c.anchor.size()) ofile << c.anchor << '\t';
+	    else ofile << "n.a." << '\t';
 	    ofile << geneInfo[gRegions[refIndex][i].lid].barcode << '\t';
-	    ofile << c.spacerright << '\t';
+	    if (c.spacerright.size()) ofile << c.spacerright << '\t';
+	    else ofile << "n.a." << '\t';
 	    ofile << padlock << '\t';
 	    ofile << arm1TM << '\t' << arm2TM << '\t' << barTM << '\t' << probeTM << '\t';
 	    ofile << arm1GC << '\t' << arm2GC << '\t' << barGC << '\t' << probeGC << std::endl;
@@ -420,10 +424,13 @@ namespace dicey
 	      rcfile << "\"" << gRegions[refIndex][i].strand << "\", ";
 	      rcfile << "\"" << c.chrname[refIndex] << ':' << gRegions[refIndex][i].start + 1 << '-' << gRegions[refIndex][i].end + 1 << "\", ";
 	      rcfile << "\"" << arm1 << '-' << arm2 << "\", ";
-	      rcfile << "\"" << c.spacerleft << "\", ";
-	      rcfile << "\"" << c.anchor << "\", ";
+	      if (c.spacerleft.size()) rcfile << "\"" << c.spacerleft << "\", ";
+	      else rcfile << "\"n.a.\", ";
+	      if (c.anchor.size()) rcfile << "\"" << c.anchor << "\", ";
+	      else rcfile << "\"n.a.\", ";
 	      rcfile << "\"" << geneInfo[gRegions[refIndex][i].lid].barcode << "\", ";
-	      rcfile << "\"" << c.spacerright << "\", ";
+	      if (c.spacerright.size()) rcfile << "\"" << c.spacerright << "\", ";
+	      else rcfile << "\"n.a.\", ";
 	      rcfile << "\"" << padlock << "\", ";
 	      rcfile << "\"" << arm1TM << "\", ";
 	      rcfile << "\"" << arm2TM << "\", ";