#!/usr/bin/perl -w

use strict;

my $seq="APKLGIYSPRIGLYHFHKLDTPRLGAKLJHHDGFYSDA";
my @motif=("ST","P","RK","ILVF","G","ILVFM","Y");
my @a = my @b = my @c = @motif; my %m;

while(my$r=!$|++&&\@a||pop@a&&\@a||shift@b&&\@b){for(glob('{'.
join('',map{'{'.(join',',split(//)).'}'}@$r).'}')){length($_)>
2&&$seq=~/$_/&&$m{$_}++;}}for(sort{length($b)<=>length($a)}keys
%m){print"$_ at ",index($seq,$_)+1,"\n"}

=OUTPUT
SPRIGLY at 8
PRIGLY at 9
PKLGIY at 2
SPRIGL at 8
KLGIY at 3
RIGLY at 10
SPRIG at 8
TPRLG at 21
TPRL at 21
IGLY at 11
LGIY at 4
SPRI at 8
GFY at 33
GIY at 5
TPR at 21
GLY at 12
SPR at 8