Ummm, why don't you put the results into a hash instead?

my %freq;

...

my $token = $genome[$i] . $genome[$i+1];
$freq{$token}++;
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For example, if your input sequence is 'abbca', while you step through the sequence, you will get -

$freq{ab}++;
$freq{bb}++;
$freq{bc}++;
$freq{ca}++;
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