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#!/usr/bin/perl
use strict;
...
    print "the regex code took:",timestr(timediff($a3_n, $a3_0)),"\n";
}

my (@keys)= keys %DNA_sequence_count;
foreach my $key (@keys) {
...
    ++$DNA_sequence_count{substr($allbuffered, -$j, $i)};
  }
}

CATCAT
gives
...
C 2
A 2 (from AT at the end)
T 2 (from TCA + last T)