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

use Benchmark;

use Data::Dumper;

my $DNAlength= 600000;
my $sequencelength= 3;
my $testfilename= 'DNA.tst';
my $bufsize= 1024;

# create testdata
open(my $testfile, ">$testfilename") or die "$testfilename: $!";
my $buffer = '';
for (my $i=$DNAlength; $i; --$i) {
	$buffer.= qw(A C G T)[rand 4];
	if (length($buffer) > $bufsize) {
		print $testfile $buffer;
		$buffer = '';
	}
}
print $testfile $buffer;
close $testfile;

a1: {
	# Start collecting data
	my %DNA_sequence_count;
	
	my $a1_0=new Benchmark;
	open($testfile, $testfilename) or die "$testfilename: $!";
	my $kept=0;
	while (1) {
		my $read_bytes = read($testfile, $buffer, $bufsize-$kept);
		last unless $read_bytes;
		my $end_buffer = $read_bytes-$sequencelength;
		for (my $i=0; $i <= $end_buffer; ++$i) {
			++$DNA_sequence_count{substr($buffer, $i, $sequencelength)};
		}
		$kept= $sequencelength-1;
		$buffer= substr($buffer, $end_buffer+1, $kept);
	}
	close $testfile;
	my $a1_n=new Benchmark;
	
	print "the file code took:",timestr(timediff($a1_n, $a1_0)),"\n";
}

a2: {
	# Start collecting data
	my %DNA_sequence_count;
	
	my $a2_0=new Benchmark;
	open($testfile, $testfilename) or die "$testfilename: $!";
	my $allbuffered= <$testfile>;
	close $testfile;
	my $end_buffer= length($allbuffered)-$sequencelength+1;
	for (my $i=0; $i <= $end_buffer; ++$i) {
			++$DNA_sequence_count{substr($allbuffered, $i, $sequencelength)};
	}
	my $a2_n=new Benchmark;

	print "the scalar code took:",timestr(timediff($a2_n, $a2_0)),"\n";
}

a3: {
	# Start collecting data
	my %DNA_sequence_count;
	
	my $a3_0=new Benchmark;
	open($testfile, $testfilename) or die "$testfilename: $!";
	my $allbuffered= <$testfile>;
	close $testfile;
	++$DNA_sequence_count{$1.$2} while $allbuffered=~ /(.)(?=(..))/g;
	my $a3_n=new Benchmark;

	print "the regex code took:",timestr(timediff($a3_n, $a3_0)),"\n";
}


##</code><code>##

my (@keys)= keys %DNA_sequence_count;
foreach my $key (@keys) {
  for ($i=$sequencelength-1; $i; --$i) {
    $DNA_sequence_count{substr($key, 0, $i}+= $DNA_sequence_count{$key};
  }
}
# correction again thanks to ikegami!
for ($i=$sequencelength-1; $i; --$i) {
  # second correction thanks to sauoq
  for ($j=$i; $j<$sequencelength; ++$j) {
    ++$DNA_sequence_count{substr($allbuffered, -$j, $i)};
  }
}

##</code><code>##

CATCAT
gives
CAT 2
ATC 1
TCA 1

Applying that algorithm you get
CA 2 (directly from CAT)
AT 2 (from ATC + AT at the end)
TC 1 (directly from TCA)
C 2
A 2 (from AT at the end)
T 2 (from TCA + last T)