my %count;

my $length = length $seq;
for my $i (0 .. $length - 3) {
  $count{ substr($seq, $i, 1) }++;
  $count{ substr($seq, $i, 2) }++;
  $count{ substr($seq, $i, 3) }++;
}

$count{ substr($seq, $length - 1, 1) }++;
$count{ substr($seq, $length - 2, 1) }++;
$count{ substr($seq, $length - 2, 2) }++;