Finding 2000 bp sequences that occur more than once in the genome I am looking for a software that can identify long sequences (1500-2000 bp) that occur more than once in my genome of interest. A k-mer counter like KMC could have worked, but KMC has a max limit of 256 bp. If I can club contiguous 256-mers from KMC, that would work too, but I don't know how to do that. Any ideas?
MUMmer includes a repeat-match tool which can do exactly that:
$ repeat-match
USAGE:  repeat-match  [options]  &lt;genome-file&gt;

Find all maximal exact matches in &lt;genome-file&gt;

Options:
 -E    Use exhaustive (slow) search to find matches
 -f    Forward strand only, don't use reverse complement
 -n #  Set minimum exact match length to #
 -t    Only output tandem repeats
 -V #  Set level of verbose (debugging) printing to #

Note that a &quot;maximal exact match&quot; is just a maximal repeat.