#!/usr/bin/perl

use strict;
use warnings;

my $seq="ASPTFHKLDTPRLAKLJHHDFSDA";
my @pattern=("ST","P","RK","ILVF");

# array of refs to arrays of redundant 
# residues within the pattern
my @patternarray;

for (my $e=0;$e<=$#pattern;$e++){
    my @elementarray= split (/ */, $pattern[$e]);
    $patternarray[$e]=\@elementarray;
}

my $found;
my $lastmatchpos;
LOOP: until ($found){

    # deal with the first residue match as a special case

    my @resarray=@{$patternarray[0]};   
    $seq=~ /([@resarray])/gc;
    die("Sequence does not contain requested motif.\n") unless $1;  
    $found = $1;
    $lastmatchpos=pos($seq);
    
    # all the other residues in the pattern

    for (my $e=1;$e<=$#patternarray;$e++){
        my @resarray=@{$patternarray[$e]};
        if ($seq=~ /\G([@resarray])/gc){
            $found .= $1;
        }else{     #reset matching algorithm
            my $newmatchpos=$lastmatchpos+1;
            last if ($newmatchpos > length($seq));
            pos($newmatchpos);
            $found='';
            next LOOP;
        }
    }

}

print ("$found at $lastmatchpos\n");