#! perl -slw
use strict;
use Data::Dumper;

my $site1 = 'abcdecdefgefghi';
my $site2 = 'zyxwvxwvutvutrs';

# brute force
my (%hash, $loops);
for my $base1( split //, $site1 ) {
    for my $base2( split //, $site2 ) {
        $hash{"${base1}_$base2"}++;
        $loops++;
    }
}

print Dumper \%hash;
__DATA__
$VAR1 = {
          'f_r' => 2,
          'c_s' => 2,
          'd_w' => 4,
          'c_z' => 2,
          'e_r' => 3,
          'i_v' => 3,
          'g_w' => 4,
          'h_x' => 2,
          'f_t' => 4,
          'i_r' => 1,
          'h_r' => 1,
          'h_w' => 2,
          'c_u' => 4,
          'a_y' => 1,
          'd_s' => 2,
          'i_u' => 2,
          'c_v' => 6,
          'c_y' => 2,
          'b_s' => 1,
          'a_t' => 2,
          'h_t' => 2,
          'b_z' => 1,
          'i_z' => 1,
          'f_s' => 2,
          'i_x' => 2,
          'h_u' => 2,
          'c_w' => 4,
          'a_x' => 2,
          'g_x' => 4,
          'a_r' => 1,
          'b_w' => 2,
          'e_u' => 6,
          'a_u' => 2,
          'e_v' => 9,
          'b_x' => 2,
          'i_t' => 2,
          'a_z' => 1,
          'd_v' => 6,
          'b_r' => 1,
          'c_t' => 4,
          'g_s' => 2,
          'b_u' => 2,
          'i_w' => 2,
          'd_t' => 4,
          'i_s' => 1,
          'a_v' => 3,
          'f_w' => 4,
          'h_v' => 3,
          'g_y' => 2,
          'h_s' => 1,
          'a_s' => 1,
          'g_r' => 2,
          'c_x' => 4,
          'f_x' => 4,
          'd_z' => 2,
          'd_u' => 4,
          'g_t' => 4,
          'g_u' => 4,
          'h_z' => 1,
          'f_y' => 2,
          'g_z' => 2,
          'c_r' => 2,
          'b_t' => 2,
          'b_y' => 1,
          'd_y' => 2,
          'e_s' => 3,
          'b_v' => 3,
          'i_y' => 1,
          'e_y' => 3,
          'e_x' => 6,
          'f_u' => 4,
          'g_v' => 6,
          'd_r' => 2,
          'f_v' => 6,
          'h_y' => 1,
          'e_w' => 6,
          'a_w' => 2,
          'e_z' => 3,
          'f_z' => 2,
          'd_x' => 4,
          'e_t' => 6
        };