Is there an open source standalone tool that finds de novo direct interspersed DNA repeats in a small sequence and allows for mismatches? Something similar to repeat-match.
Is that helpful? Searching Repeats And Palindromic Sequences In Dna Sequences
I saw that post already and it was very helpful. I went through the tools and that's how I found repeat-match via the MUMmer answer. Unless I'm mistaken, the only tool I found that matches what I'm looking for (direct interspersed repeats, not tandem or consecutive repeats) is REPuter but it requires a license for the standalone version. My sequence is small and not a genome. I'll add more details to my question.
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