I'm trying to analyze fragments generated from in silico digests of two draft genomes to determine how many of the fragments differ between the two species. For input, I have two unordered lists of ~5,000 ~300bp fragments (one from each species); I would like to determine how many of them are identical, how many differ by 1 base, 2, 3, etc., and how many don't have a corresponding fragment in the other genome.
Is this possible? What approach should I take? I can't seem to figure out if pairwise aligners will handle unordered lists like this, or if multiple alignment is what I need, or if I just want to map both sets back to one of the reference genomes. I'm not very experienced at this but I'd like to learn.