#! perl -slw
use strict;
use List::Util qw[ min ];
use Data::Dumper;

my @site1 = qw[ abcde cdefg efghi ];
my @site2 = qw[ zyxwv xwvut vutrs ];

my %counts;
for my $site1 ( @site1 ){
    for my $site2 ( @site2 ) {
        $counts{ substr( $site1, $_, 1 ) . substr( $site2, $_, 1 ) }++
+ 
            for 0 .. min( length( $site1 )-1, length( $site2 )-1 );
    }
}

print Dumper \%counts;
__END__
P:\test>400340.pl
$VAR1 = {
          'bu' => 1,
          'cv' => 2,
          'fu' => 2,
          'av' => 1,
          'hw' => 1,
          'ax' => 1,
          'du' => 2,
          'gv' => 2,
          'es' => 1,
          'is' => 1,
          'ct' => 1,
          'iv' => 1,
          'gx' => 1,
          'fr' => 1,
          'cx' => 2,
          'dy' => 1,
          'az' => 1,
          'ev' => 3,
          'ez' => 1,
          'et' => 2,
          'it' => 1,
          'dw' => 2,
          'hu' => 1,
          'dr' => 1,
          'ex' => 2,
          'fy' => 1,
          'cz' => 1,
          'by' => 1,
          'fw' => 2,
          'bw' => 1,
          'gs' => 1,
          'hr' => 1,
          'gt' => 2
        };
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