Answers.Body: <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>
  
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Answers.Text: This looks ideal. Will try this out and update. Thank you!
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Answers.Text: 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
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Body: <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>
  
Tags: <phylogenetics><k-mer><repeat-elements><sequence-homology>
Title: Finding 2000 bp sequences that occur more than once in the genome
ThreadText: # Finding 2000 bp sequences that occur more than once in the genome
  
  (Asked by: username_0 on 2021-05-03)
  
  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?
  
  **Tags:** phylogenetics, k-mer, repeat-elements, sequence-homology
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-05-04. Score: 3 | Accepted answer
  
  [MUMmer](https://mummer4.github.io/manual/manual.html) 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.
  
  > **Comments:**
  > **username_0**: This looks ideal. Will try this out and update. Thank you!  
  > **username_0**: 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  
  
  ---
  
  