my $orig = <DATA>;

my $i = 0;
while (<DATA>) {
	my $matches = $orig ^ $_;
	printf "Sequence %d has %d identities\n", $i++, $matches =~ tr/\0//;	
}

__DATA__
ATCGGGACG 
TCGTCAGCG
ATGCGAAAA


##</code><code>##

Sequence 0 has 2 identities
Sequence 1 has 4 identities