I have one long sequence (several kb) (I can cut it into pieces) and I want to find small parts that align (small repeats, from 10 to 500 bp long). What is the best algorithm to use? why? Preferably I want to use inside my python script.
It should allow mismatches and gaps with a penalty (maybe 1 mismatch in 10 bp, one gap).
I've tried pairwise2.align.localxx, but it gave me very long alignments as output.