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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.

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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.

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RepeatFinder may suffice by Volfovsky et al. (2001) and is available for download.

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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.

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