use strict;
use warnings;

use Algorithm::Loops qw( MapCar );

my @site1 = qw(
   AATKKM
   123456
);

my @site2 = qw(
   GGGGGG
   !@#$%^
);

my $site1;
my $site2;

my @pairs;
my %counts;

foreach $site1 (@site1) {
   my @site1_parts = split(//, $site1);

   foreach $site2 (@site2) {
      my @site2_parts = split(//, $site2);

      MapCar { $counts{$_[0].$_[1]}++ }
         \@site1_parts, \@site2_parts;
   }
}

print($_, ': ', $counts{$_}, $/) foreach (sort keys %counts);

__END__
output
======
1!: 1
1G: 1
2@: 1
2G: 1
3#: 1
3G: 1
4$: 1
4G: 1
5%: 1
5G: 1
6G: 1
6^: 1
A!: 1
A@: 1
AG: 2
K$: 1
K%: 1
KG: 2
MG: 1
M^: 1
T#: 1
TG: 1