Some genome sequence share a counter. I mapped each genome sequence to the reference of the update counter, so there is some dereferencing.

Chris

#!/usr/bin/perl
use strict;
use warnings;

my @genome = ('a', 'a');
my $i = 0;

my @seq = qw/ aa ag ac at ta tg tc tt ca cg cc ct ga gg gc gt /;
my ($tt, $ag, $ac, $at, $ta, $tg, $ga, $cg, $cc, $gc) = (0) x 10;
my %counter;
@counter{@seq} = \($tt, $ag, $ac, $at, $ta, $tg, $ga, $tt, 
                  $tg, $cg, $cc, $ag, $ga, $cc, $gc, $ac);            
+      

if (exists $counter{ $genome[$i] . $genome[$i+1] }) {                 
+                   
    ++${ $counter{ $genome[$i] . $genome[$i+1] }} 
}
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