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sub mismatches {
  my($source, $target) = @_;
...
  my %seen = map +($_ => 1), $s =~ /[^\[\]]/g;
  scalar grep $seen{$_}, $t =~ /[^\[\]]/g;
}

my %bits = ('A' => 1, 'C' => 2, 'G' => 4, 'T' => 8);
my $source1 = bitwise('[TCG]GGGG[AT]');
...
    chr($char)
  } $string =~ /(\[.*?\]|.)/g;
}