text: user4617: The repeat masker site has a size limit of 90kb. 
  Where can I mask repeats in a 500kb sequence?
  Ideally, I need a thorough repeat masking of known and de-novo found repeats of various complexity. I am working on Windows but can access Unix too.
  
  user3384: From: http://meme-suite.org/doc/glam2_tut.html, here's a few tools that do various repeat masking tasks.
  
  These tools mask various kinds of repeats: Repeatmasker, Censor, seg/pseg/nseg, DUST,
        XNU, DSR, GBA.
  
  Censor, seg/pseg/nseg, dust, DSR all have locally available applications. DSR, GBA, and CAST are algorithms for repeat masking.
  
  user4686: RepeatFinder may suffice by Volfovsky et al. (2001) and is available for download.
  
  user77: RepeatMasker can downloaded an run locally. There's then no size limit, though do note that it's quite slow for mammalian-sized sequences (you'll want to split it into chunks and run in parallel in such cases). For a small 500kb sequence that won't pose an issue.
  
original_text: 4617: <p>The <a href="http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker" rel="nofollow noreferrer">repeat masker site</a> has a size limit of 90kb. 
  Where can I mask repeats in a 500kb sequence?</p>
  
  <p>Ideally, I need a thorough repeat masking of known and de-novo found repeats of various complexity. I am working on Windows but can access Unix too.</p>
   3384: <p>From: <a href="http://meme-suite.org/doc/glam2_tut.html" rel="nofollow noreferrer">http://meme-suite.org/doc/glam2_tut.html</a>, here's a few tools that do various repeat masking tasks.</p>
  
  <blockquote>
    <p>These tools mask various kinds of repeats: <a href="http://www.repeatmasker.org/" rel="nofollow noreferrer">Repeatmasker</a>, <a href="http://www.girinst.org/censor/" rel="nofollow noreferrer">Censor</a>, <a href="ftp://ftp.ncbi.nih.gov/pub/seg/" rel="nofollow noreferrer">seg/pseg/nseg</a>, <a href="http://meme-suite.org/doc/dust.html" rel="nofollow noreferrer">DUST</a>,
        <a href="http://meme-suite.org/doc/purge.html" rel="nofollow noreferrer">XNU</a>, <a href="https://www.liebertpub.com/doi/abs/10.1089/106652703321825955" rel="nofollow noreferrer">DSR</a>, <a href="https://academic.oup.com/bioinformatics/article/22/24/2980/208627" rel="nofollow noreferrer">GBA</a>.</p>
  </blockquote>
  
  <p>Censor, seg/pseg/nseg, dust, DSR all have locally available applications. DSR, GBA, and CAST are algorithms for repeat masking.</p>
   4686: <p><a href="http://www.cbcb.umd.edu/software/RepeatFinder/" rel="nofollow noreferrer">RepeatFinder</a> may suffice by Volfovsky et al. (2001) and is available for download.</p>
   77: <p><a href="http://www.repeatmasker.org/RMDownload.html" rel="nofollow noreferrer">RepeatMasker</a> can downloaded an run locally. There's then no size limit, though do note that it's quite slow for mammalian-sized sequences (you'll want to split it into chunks and run in parallel in such cases). For a small 500kb sequence that won't pose an issue.</p>
  