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For each position in the given sequences it is randomly determined with
probability (mutation rate / 100) if the given position is mutated. If so, in
80% of the cases a substitution is performed, in 10% an insertion, and in 10% a
deletion, respectively. For substitution and insertion events, the nucleotide is
generated randomly without regard to the original nucleotide. That is,
resubstitutions are possible. This procedure equals the one described on page
1867 of the following paper

T.D. Wu and C.K. Watanabe. GMAP: a genomic mapping and alignment program for
mRNA and EST sequences. Bioinformatics, 21(9):1859-1875, 2005.]])