Hi,
I have a set of piRNAs in fasta format and I want to find their potential targets.
According to literature nucleotides in position 1-10 in the piRNAs sequences should constitute the seed and do not tolerate any mismatch while nt 11-20 tolerate up to 3 mismatches.
Bowtie can specify the length of the seed, but I'm having troubles finding the right combination of parameters to translate the piRNA target pairing logic into a single bowtie command line.

Is there any solution to get this done with a single alignment run or do I have to run a first alignment guided by the seed 1-10nt, and successively another alignment for the 11-20 region allowing for up to 3 mismatches?

Thank you in advance for your help!
Or maybe you can use [LAST](http://last.cbrc.jp) with a custom [seeding scheme](http://last.cbrc.jp/doc/last-seeds.html) ?