my ($a,$c,$g,$t) = (0, 0, 0, 0);

##</code><code>##

my $a = 0;
my $c = 0;
my $g = 0;
my $t = 0;

##</code><code>##

sub comNucCount {
    my($string1, $string2) = @_;
    $string1 = uc $string1;
    $string2 = uc $string2;

    my %counts = map { $_ => 0 } qw( A C G T );

    for my $position (0 .. length($string1)-1) {
        my $char = substr($string1,$position,1);
        $counts{$char}++
            if substr($string2, $position, 1) eq $char;
    }

    return "A=$counts{A}, C=$counts{C}, G=$counts{G}, T=$counts{T}";
}

##</code><code>##

sub comNucCount {
    my($string1, $string2) = @_;
    $string1 = uc $string1;
    $string2 = uc $string2;

    my @letters = qw( A C G T )
    my %counts = map { $_ => 0 } @letters;

    for my $position (0 .. length($string1)-1) {
        my $char = substr($string1,$position,1);
        $counts{$char}++
            if substr($string2, $position, 1) eq $char;
        }
    }

    return join ', ',
           map { "$_=$counts{$_}" }
           @letters;
}