sub WEED {
 # this sets up that we will perform this for each fasta sequence in whatever
 # file.  makes the rest of the sub one step simpler.
 FASTA: for my $fastaseq (keys %matches) {
   $setscounter = 0;
   SITE: for my $site (sort {$a <=> $b } keys %{$matches{$fastaseq}}) {
     ELEM: for my $i (@{$matches{$fastaseq}{$site}}) {
       $lowerlimit = $matches{$fastaseq}{$site}[$i];
       $upperlimit = $span + $lowerlimit;
       SITEKEY: for my $sitekey (sort {$a <=> $b } keys %{$matches{$fastaseq}}) {
         SET: for $setcount (@{$matches{$fastaseq}{$sitekey}}) {
           if ($setcount >= $lowerlimit || $_ <= $upperlimit) {
             push @{$sets{$fastaseq}[$setscounter]{$sitekey}}, $setcount;
             #closes If setcount
             }
           next SET;
           #closes For setcount
           }
         next SITEKEY;  
         #closes SITEKEY  
         }    
       next ELEM;
       # closes for my i
       }
     $setscounter++;
     next SITE;
     #closes for my site
     }
   next FASTA;
   #closes for my fastaseq
   }
 return %sets;
 #closes subroutine
 }