your solution is missing some possibilities.

Well, I implemented (on purpose) exactly the list the OP asked for.  It can of course be extended, if so desired:

my @cnt = qw(A2G G2A C2T T2C A2T A2C G2T G2C ...);
[download]

Alternatively, simply compute the full matrix of count routines:

#!/usr/bin/perl -w
use strict;

my %cnt;
my @c = qw(A T C G);
for my $c1 (@c) {
    for my $c2 (@c) {
        next if $c1 eq $c2;
        (my $t = $c2) =~ tr/ATCG/HRDZ/;
        my $x = $c1 ^ $t;
        $cnt{$c1."2".$c2} = eval "sub { \$_[0] =~ tr/$x/$x/ }";
    }
}

my $seq1 = 'AAAACCCCGGGGTTTT';
my $seq2 = 'ACGTACGTACGTACGT';

(my $tmp = $seq2) =~ tr/ATCG/HRDZ/;
my $diff = $seq1 ^ $tmp;
    
print join("; ", map { $_."=".$cnt{$_}->($diff) } sort keys %cnt ), ".
+";

__END__
A2C=1; A2G=1; A2T=1; C2A=1; C2G=1; C2T=1; G2A=1; G2C=1; G2T=1; T2A=1; 
+T2C=1; T2G=1.
[download]