Is this the kind of thing you are doing? 

#!/usr/bin/perl -l

use strict;
use warnings;

my $k = 5;

my $file1contents = 'TACATCTCAAAACACTTTCATCTCACGACTACTACTACTACTTCAAAAC
+ACCATCAT';
my $file2contents = 'ACTTCAACATAACTACTATATACTACTCATACTACTACTCTTAAAACTA
+CTATACTA';

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

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

[download]

In reply to Re: FInding the longest match from an initial match between two files by tybalt89
in thread FInding the longest match from an initial match between two files by Allie_grater

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