This will perform the same job, but run significantly faster (Approx 7 hours). 

$| = 1;
my $compare_count = 0;
for (my $i = 0; $i < @kmers; $i++ ) {
    for (my $j = $i + 1; $j < @kmers; $j++ ) {
        my $sims = ( $kmers[ $i ] ^ $kmers[ $j ] ) =~ tr[\0][];
        if(  $sims == 19 ) {
            print "Match found: $kmers[ $i ], $kmers[ $j ]";
            push @varient_kmers, ($kmers[$i], $kmers[$j]);
        }
        ++$compare_count;
    }
}
print "\rFinished: $compare_count comparisions made.\n";

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In reply to Re: Comparing a large set of DNA sequences by BrowserUk
in thread Comparing a large set of DNA sequences by shamshersingh

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