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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?

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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.

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    $\begingroup$ This looks ideal. Will try this out and update. Thank you! $\endgroup$ – PSiddy May 4 at 15:31
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    $\begingroup$ 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 $\endgroup$ – PSiddy May 5 at 22:24

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