Uhm... let me think... file is huge, so it is not advisable to keep all the non-repeated sequences inside a hash, or your memory will blow.

I think it would be a good idea to use a message digest on the values to keep memory occupation low (at the expense of some CPU, of course); this also exposes you to the risk of two different sequences having the same digest -the probability should be low, but not null...

I have no data to test and I never used Digest::MD5 directly, so take the subsequent code as a suggestion -it may suit your needs or be completely wrong. I'm looking at the documentation on http://search.cpan.org/doc/GAAS/Digest-MD5-2.20/MD5.pm

    use strict ;
    use warnings ; # ...if you have Perl 5.6

    # read from stdin, spit data to stdout
    # (just to keep it simple)
    use Digest::MD5 qw(md5_hex) ; # or one of md5*'s

    my %digests ;

    while (my $line = <STDIN>) {
      my $dig = md5_hex($line) ;
      if (exists $digests{$dig}) {
        print STDERR "WARNING: duplicated checksum $dig for line $line
+\nWARNING: skipping $line\n" ;
         $digest{$dig}++ ; # you can use this to count repetitions
      } else {
        $digest{$dig} = 0 ;
        print $line ;
      }
    }
[download]

If this not what you need, I hope that at least this can help you to reach the better solution.