#!/usr/bin/perl -l

use strict;
use warnings;

my $k = 5;

my $file1contents = 'TACATCTCAAAACACTTTCATCTCACGACTACTACTACTACTTCAAAACACCATCAT';
my $file2contents = 'ACTTCAACATAACTACTATATACTACTCATACTACTACTCTTAAAACTACTATACTA';

$_ = "$file1contents\n$file2contents";

print "at position $-[0] is match $1" while /(?= (.{$k,}) .* \n .* \1 )/gx;

##</code><code>##

at position 8 is match AAAAC
at position 27 is match ACTACTACT
at position 28 is match CTACTACT
at position 29 is match TACTACTACT
at position 30 is match ACTACTACT
at position 31 is match CTACTACT
at position 32 is match TACTACTACT
at position 33 is match ACTACTACT
at position 34 is match CTACTACT
at position 35 is match TACTACT
at position 36 is match ACTACT
at position 37 is match CTACT
at position 39 is match ACTTCAA
at position 40 is match CTTCAA
at position 41 is match TTCAA
at position 44 is match AAAAC