<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>

CC BY-SA 4.0
2021-05-04T15:31:01.030Z
This looks ideal. Will try this out and update. Thank you!
PSiddy
CC BY-SA 4.0
2021-05-05T22:24:49.737Z
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
PSiddy
CC BY-SA 4.0
2021-05-04T03:38:13.037Z
2021-05-04T03:38:13.037Z
Throckmorton
<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>

<phylogenetics><k-mer><repeat-elements><sequence-homology>
Finding 2000 bp sequences that occur more than once in the genome
# 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

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## 1 answers

### Answer by username_1 on 2021-05-04. Score: 3 | Accepted answer

MUMmer includes a repeat-match tool which can do exactly that:
$ repeat-match
USAGE:  repeat-match  [options]  

Find all maximal exact matches in 

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  

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