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############# Begin WEED subroutine ##############      
      
...
 }

############# End WEED subroutine ################

          for my $hit (@{$matches{$fasta_id}{$sitekey}}) {
            next unless ($hit >= $lowerlimit);
            last unless ($hit <= $upperlimit);

sub WEED {

...
 return %sets;
 #closes subroutine
 }