@{ $sets{ $fasta_id }[ $setscounter ]{ $sitekey } } = grep {
    $_ >= $lowerlimit and $_ <= $upperlimit
} @{ $matches{ $fasta_id }{ $sitekey } }

unless( @{ $sets{ $fasta_id }[ $setscounter ]{ $sitekey } } ) {
    undef $sets{ $fasta_id }[ $setscounter ] };
    next WEEDLOW;
}