thanks again ikegami and all for your help. I am a beginner at perl so I 've been trying to answer my questons, but it was no good. I have another one for you, which might be a bit trickier. I need to calculate the frequencies by which specific combinations appear. So after I do the pairwise combinations and store them into the @count _collection(that is all the possible times that specific combinations appear, then I have to do that for individual sites and calculate the frequency. In the code that is if a divide a specific counter (say counterAG) from %counts with how many times it appears in the AoH. That is I need to calulate countAG/total_count_AG. I don't know if this is possible, I suspect that since the keys of the hashes are similar, it can be done, but I am not sure how. Once again thanks for your patience and your time. 
use strict;
use warnings;

my @site1 = qw(
   AATKKM
   AKTKKM
);

my @site2 = qw(
   GGGGGG
   HHHHHH
);

my $site1;
my $site2;

my @pairs;
my @count_collection;

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

   my %counts;

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

      my $i = @site1_parts;
      $counts{$site1_parts[$i].$site2_parts[$i]}++ while ($i--);
   }

   push(@count_collection, \%counts);
}

foreach (@count_collection) {
   my $counts = $_;
   print($_, ': ', $counts->{$_}, $/) foreach (sort keys %$counts);
   print($/);
}

__END__
output
======
AG: 2
AH: 2
KG: 2
KH: 2
MG: 1
MH: 1
TG: 1
TH: 1

AG: 1
AH: 1
KG: 3
KH: 3
MG: 1
MH: 1
TG: 1
TH: 1

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In reply to again regarding pairwise comparisons between strings and arrays by replicant4

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