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

##</code><code>##

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