This method allows to find duplicates on the string and doesn't suffer from memory limitations, though it could be much slower than the hash based solution.

The trick is to do a block sorting on the sequence on chunks of limited size. The sorted indexes of every chunk are saved to disk on different files and finally merged sequentially to look for duplicates.

Also, once the block sorting process has been done, looking for repeated sequences of different lenghts is relatively cheap.

use strict;
use warnings;

my $size = 12;

use Sys::Mmap;
use Sort::Key::Merger 'keymerger';

$| = 1;

open BIG, '<', 'big.txt'
    or die "unable to open big.txt";

mmap(my $big, 0, PROT_READ, MAP_SHARED, *BIG)
    or die "unable to mmap big.txt";

my $chunk = 8 * 1024 * 1024;

my @files;
my $n = 0;

my $lenbig = length $big;

for (my $i = 0; $i < $lenbig; $i += $chunk) {
    my $top = $i + $chunk;
    $top = $lenbig if $lenbig < $top;

    print STDERR "sorting from $i to $top\n";

    my @s = sort { ( substr($big, $a, 30) cmp substr($big, $b, 30) or
             substr($big, $a, 10_000) cmp substr($big, $b, 10_000) or
             substr($big, $a, 16_000_000) cmp substr($big, $b, 16_000_
+000) or
             substr($big, $a) cmp substr($big, $b) ) } $i..($top);

    my $file = "small.$i";
    push @files, $file;

    open F, '>', $file
    or die "unable to open $file";
    print F pack(N => $_) for @s;
    close F;
}

my @fh;
for (@files) {
    open my $fh, '<', $_
    or die "unable to open $_";
    push @fh, $fh;
}

my $merger = keymerger {
    if (read $_, my $data, 4) {
    my $i = unpack N => $data;
    return (substr($big, $i, $size), $i);
    }
    else {
    return ()
    }
} @fh;

my $last = $merger->();
my $count = 1;
while (defined(my $i = $merger->())) {
    # print substr($big, $i, $size), "\n";
    if (substr($big, $i, $size) eq substr($big, $last, $size)) {
    $count++;
    }
    else {
    if ($count > 1) {
        print substr($big, $last, $size), " appears $count times\n";
    }
    $last = $i;
    $count = 1;
    }
}

if ($count > 1) {
    print substr($big, $last, $size), " appears $count times\n";
}
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