wrong boxb found with newest code

[phycologia]

previous version(s?) of the code identified boxb correctly, but now identifies incorrect sequences as boxb; all begin with "TAGCA"
accession numbers for sequences with this issue (all in order Nostocales):
KF417427.1
MK953008.1
MN15981.1

[callmcgovern]

@phycologia ; what does boxb end with in these cases?

[phycologia]

TGCTG! @callmcgovern

[nlabrad]

Can you paste what it's supposed to be? @phycologia

[nlabrad]

I think I'm making progress on this one. It was actually BIG. It uncovered that it could be a problem in the future with other sequences. I have a working prototype of yet another algorithm but I think it's more robust now.

[nlabrad]

@phycologia @callmcgovern I think this is fixed. I ran a test and it found the one @phycologia wanted above alongside another possible one. I set the BoxB length limit to 60 bases or you'd get a bunch more. I don't think they are ever that long, but keep an eye out.

[nlabrad]

MN15981.1

was not found in genbank btw. The other two worked.

[phycologia]

@nlabrad ah my bad I was with fam for the weekend so I didn't your first comment til now! It sounds like you got it figured out, but just in case:
MK953008.1 proper box b is TAGCACCTGAAAGCAAAAAAGTCAGACTGCTG
KF417427.1 proper box b is TAGCACCTGAGATCAAAGAATCAGACTGCTG
MN152981.1 (my b on the typo) proper box b is TAGCAACTGGATGATAAAGAATCAGACTGCTG
what was BIG?! this sounds juicy

[nlabrad]

seems to be working for the first two, but for the last one I get
BoxB:
Sequence CAGCGTATATTGAACAGAGATTGTTAACTGTTGAGTGTAGGCTG
Length: 44

    Thoughts?

[phycologia]

huh, I'm not sure!