text: user12127: 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?
  
  user6628: 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.
  
original_text: 12127: <p>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?</p>
   6628: <p><a href="https://mummer4.github.io/manual/manual.html" rel="nofollow noreferrer">MUMmer</a> includes a <code>repeat-match</code> tool which can do exactly that:</p>
  <pre><code>$ 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 #
  </code></pre>
  <p>Note that a &quot;maximal exact match&quot; is just a maximal repeat.</p>
  