[Genome] blat -minIdentity

[Yueming Ding]

Generator Microsoft Word 11 (filtered medium) Hi I have a problem with - minIdentity in using blat. I tried the following command line:
blat mouse_genome.fa seqs.fa seqs.psl - minScore=20 - noHead - tileSize=8 - stepSize=5 - noTrimA

The seqs.fa are 25mers.

If I add - minIdentity=95, I' ll get less hits, which makes sense. But if I add - minIdentity=85, or - minIdentity=80, or - minIdentity=70, I still get the same number of hits as I used the default (- minIdentity=90). Could you please tell me why I couldn' t get more hits if I used the smaller number of - minIdentity than the default? Thanks.

Yueming Ding
The Jackson Laboratory