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

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

##</code><code>##

my %bits = ('A' => 1, 'C' => 2, 'G' => 4, 'T' => 8);
my $source1 = bitwise('[TCG]GGGG[AT]');
my $target1 = bitwise('AGGGG[CT]');
print mismatches($source, $target1), "\n";

sub mismatches {
  my($source, $target) = @_;
  ($source & $target) =~ tr/\0//;
}

sub bitwise {
  my $string = shift;
  join '', map {
    my $char = 0;
    $char |= $bits{$_} for /[ACGT]/g;
    chr($char)
  } $string =~ /(\[.*?\]|.)/g;
}