#!/usr/bin/perl -w
use strict;

my $s   = "APKLGIYSPRIGLYHFHKLDTPRLGAKLJHHDGFYSDA";
my @m = ( "ST", "P", "RK", "ILVF", "G", "ILVFM", "Y" );

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

=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