Here's essentially the same thing without __DATA__:

c:\@Work\Perl\monks>perl -wMstrict -le
"my $seq = 'ATCGGGACG';
 my $n = 0;
 ;;
 for my $s (qw(TCGTCAGCG ATGCGAAAA TTTTTTTTT TATTTTTTT)) {
   print qq{\n'$seq' original};
   my $idents = (my $same = $s ^ $seq) =~ tr/\x00//;
   $same =~ tr/\x00-\xff/^ /;
   print qq{'$s' seq }, $n++;
   print qq{ $same  $idents identities};
   }
"

'ATCGGGACG' original
'TCGTCAGCG' seq 0
        ^^  2 identities

'ATCGGGACG' original
'ATGCGAAAA' seq 1
 ^^  ^ ^    4 identities

'ATCGGGACG' original
'TTTTTTTTT' seq 2
  ^         1 identities

'ATCGGGACG' original
'TATTTTTTT' seq 3
            0 identities
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See also Special Literals in perldata.