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  • Anyone know a program to detect duplicated regions?

    Hi All,

    I'm working with on generating denovo mtDNA genomes for many species of an invertebrate taxa of the same genus. These critters have a duplicated non-coding region (~800bp) separated by ~6000bp, the problem is that the non-coding region is different in every species. Since this is not a tandem repeat, and is quite large, the microsatellite finding programs are of no use. Anyone know a program that can find these large duplicated regions?

    Cheers,

  • #2
    Why do not use Blast? If the query and the database are the same, it will find all the duplicated regions.
    Last edited by TiborNagy; 06-19-2014, 05:54 AM. Reason: misstype

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