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my $source1  = '[TCG]GGGG[AT]'; # ambiguous
my $target1   = 'AGGGG[CT]'; # No of mismatch = 1  only at position 1

sub mismatches {
    my($source, $target) = @_;
...
    
    scalar grep $tparts[$_] !~ /^$sparts[$_]/, 0 .. $#sparts;
  }