1 2 3 4 5 6 7 8 9   1 2 3 4 5 6 7 8 9   1 2 3 4 5 6 7 8 9   1 2 3 4 5 6 7 8 
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
| | | | | | | | | | | | |?|X|X|X|X|X|X|X|X|X|X|X|X|?| | | | | | | | | | | | |
+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

##</code><code>##

[ 6:53:31.34] P:\test>406836.pl 406836.25s.1000 406836.seq.1000 >406836.results
Loaded 1000 25-ers at P:\test\406836.pl line 17.
Processing sequence  1000 offset 01238

Processed 1000 sequences at P:\test\406836.pl line 48, <SEQ> line 1000.
Average length: 1016.119 at P:\test\406836.pl line 49, <SEQ> line 1000.
Total fuzzy comparisons: 992119000 at P:\test\406836.pl line 50, <SEQ> line ...

[ 7:22:03.34] P:\test>

##</code><code>##

timethis 10000, q[@m = ('acgt'x250 ) =~ m[(acgtacgtacgtacgtacgtacgta)]g ];
timethis 10000:  1 wallclock secs ( 1.16 usr +  0.00 sys =  1.16 CPU) @ 8643.04/s (n=10000)

##</code><code>##

#! perl -slw
use strict;
use bytes;
$| = 1;

our $FUZZY ||= 2;

open FUZ, '<', $ARGV[ 0 ] or die "$ARGV[ 0 ] : $!";
my %fuz;
while( <FUZ> ) {
	chomp;
	$fuz{ $_ } = '';
}

close FUZ;

warn "Loaded ${ \scalar keys %fuz } 25-ers";

open SEQ, '< :raw', $ARGV[ 1 ] or die "$ARGV[ 1 ] : $!";

my $totalLen = 0;
my $fuzzyComps = 0;
while( my $seq = <SEQ> ) {
	chomp $seq;
	$totalLen += length $seq;
	for my $offset ( 0 .. length( $seq ) - 25 ) { 
		my $ssref =  \substr( $seq, $offset, 25 );
		printf STDERR "\rProcessing sequence %5d offset %05d", $., $offset;

		for my $fuz ( keys %fuz ) {
			$fuzzyComps++;
			my $m =  25 - ( $fuz ^ $$ssref ) =~ tr[\0][\0];
						
			if( $m <= $FUZZY ) {
				
				## This stores the lineno/offset/fuzziness where each 25-er matched
				## in a compact form for further process; sorting etc.
#				$fuz{ $fuz } .= pack 'nnn', $., $offset, $m;
				
				## Or just print out the data to a file.
				print "Matched '$fuz' -v- '", 
					$$ssref,
				"' in line: $. @ $offset with fuzziness: ", $m;
			}
		}
	}
}
warn "\n\nProcessed $. sequences";
warn "Average length: ", $totalLen / $.;
warn "Total fuzzy comparisons: ", $fuzzyComps;
close SEQ;