align.seqs question

Commands in mothur
1

what does it mean when the report from align.seqs says that there is a negative length, or a negative number of gaps???

Here is a line from the align.report file that has me stumped:

FYV22AL02JQV98 0 AY349387.1 1434 kmer 6.73 needleman 231 0 143-1664 -1434 -230 0 0.00

2

I suspect there is either a problem with sequence FYV22AL02JQV98 or that you are using a template file that isn’t actually aligned. Let us know if any of these hold up.