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

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

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

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

sub comNucCount {
    my($string1, $string2) = @_;
...
           map { "$_=$counts{$_}" }
           @letters;
}