Hi all. I posted yesterday a question under the title pairwie comparisons. This solution script does answer my question, but I need a minor modiifcation if it is possible. The script that works is :
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

[download]
What I need is that every time that compare one $site from @array1, I need to reset the counters to 0 if it is possible. Then I need to add the values of the counters. Is this possible? Thanks in advance for anyone's help

In reply to a bit more help with pairwise comparisons between strings in arrays. by replicant4

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