# 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]  <genome-file>

Find all maximal exact matches in <genome-file>

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 "maximal exact match" is just a maximal repeat.

• This looks ideal. Will try this out and update. Thank you! May 4 at 15:31
• Okay I tried it out and it worked, so thank you! Ended up using mummer instead of repeat-match so as to compare between (and not within) sequences May 5 at 22:24