It took me longer than I thought to get this working last night... I therefore had to cut the actual golfing part short. Here is an updated version after spending a few minutes trimming chars.

#!/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
[download]

Basically, we loop through a set of munged @motif arrays transforming them into glob strings which happen to spit out the various substrings we're looking for.

-Blake