According to the original code there are six diferent instances which go to the same counters. Of course this is no problem, as you can combine the counters after the solution provided by Abigail-II like this:

$counts{tt} += $counts{aa};
$counts{ag} += $counts{ct};
$counts{ac} += $counts{gt};
$counts{tg} += $counts{ca};
$counts{ga} += $counts{tc};
$counts{cc} += $counts{gg};
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