I have contigs representing genes of interest that have been 454 sequenced from BAC libraries. The BAC inserts are about 100kb long and end up forming multiple contigs (about 50-100) after assembly. Among these contigs, I some contain the sequence of the gene of interest, including the introns.
I am interested in finding minisatellite repeat motifs, from 10 to 60 bp. I have tried SSR finder before (online: SSR Finder) but apparently it is only for microsatellites (2 to 5 bp). My aim is not to mask them, but to find their position and sequence.
What software would be a good choice in your opinion?