I am running a BLASTN search on a 15-nucleotide sequence with the following parameters:
expect threshold = 1000, word size = 7, match/mismatch = 1, -3, no filters or masks
I am getting only 100% identity hits. However, I am also interested in hits with mismatches or gaps in the middle of the sequence, which are not showing up in the results even when I raise the expect value or make the match/mismatch penalties less severe.
What parameters should I use to allow results with gaps to show up?