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  • rebzzy
    Junior Member
    • Jun 2011
    • 1
    #1

    % divergence default in RepeatMasker

    Hi -
    Does anyone know what RepeatMasker uses as a default for % divergence? I used the mitochondrial genome of one species to mask out mtDNA from another species using the default.
    Thanks!
    Tags: None
  • SES
    Senior Member
    • Mar 2010
    • 275
    #2
    I believe a blast score threshold is used for the cutoff, not percent identity. You can adjust the behavior of masking by changing the cutoff, or using one of the three settings for requiring either more sensitive matches ("-s") or speeding up the job and allowing less sensitive matches ("-q" and "-qq").

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