I renamed some of the variables to more appropriate names.

use strict;
use warnings;

sub get_index { $_[0] lt $_[1] ? ($_[0].$_[1]) : ($_[1].$_[0]) }

my @site1 = qw(
   AATKKM
   AKTKKM
);

my @site2 = qw(
   GGGGGG
   HHHHHH
);

my %pair_info;
my @pair_info_by_site;

{
   # Count pairs.

   my $site1;
   my $site2;

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

      my %pair_info_this_site;

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

         my $i = @site1_parts;
         while ($i--) {
            # Sort the letters of the pair.
            my $pair = get_index($site1_parts[$i], $site2_parts[$i]);

            # Add to pair count.
            $pair_info{$pair}++;

            # Add to pair count for this site.
            $pair_info_this_site{$pair}[0]++;
         }
      }

      push(@pair_info_by_site, \%pair_info_this_site);
   }
}

{
   # Calculate frequencies.

   my $pair;
   my $site;

   foreach $pair (keys(%pair_info)) {
      my $pair_count = $pair_info{$pair};

      foreach $site (@pair_info_by_site) {
         my $site_pair_count = $$site{$pair}[0];

         # Calculate the frequency for this site.
         $$site{$pair}[1] =  $site_pair_count / $pair_count;
      }
   }
}

{
   # Output everything.

   my $pair;
   my $site;

   print("Totals$/");
   print("======$/");
   foreach $pair (sort keys %pair_info) {
      printf("%s: count = %2d$/", $pair, $pair_info{$pair});
   }
   print($/);

   print("By Site$/");
   print("=======$/");
   foreach $site (@pair_info_by_site) {
      foreach $pair (sort keys %pair_info) {
         printf("%s: count = %2d   freq = %5.3f$/", $pair, @{$$site{$p
+air}});
      }
      print($/);
   }
}

__END__

Totals
======
AG: count =  3
AH: count =  3
GK: count =  5
GM: count =  2
GT: count =  2
HK: count =  5
HM: count =  2
HT: count =  2

By Site
=======
AG: count =  2   freq = 0.667
AH: count =  2   freq = 0.667
GK: count =  2   freq = 0.400
GM: count =  1   freq = 0.500
GT: count =  1   freq = 0.500
HK: count =  2   freq = 0.400
HM: count =  1   freq = 0.500
HT: count =  1   freq = 0.500

AG: count =  1   freq = 0.333
AH: count =  1   freq = 0.333
GK: count =  3   freq = 0.600
GM: count =  1   freq = 0.500
GT: count =  1   freq = 0.500
HK: count =  3   freq = 0.600
HM: count =  1   freq = 0.500
HT: count =  1   freq = 0.500
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