for my $hit ( @{ $matches{ $fasta_id }{ $sitekey } } ) {
     next unless $hit >= $lowerlimit;
     last unless $hit <= $upperlimit;
     push @arrayA, $hit + 0;
}
if( @arrayA ) {
    @{ $sets{ $fasta_id }[ $setscounter ]{ $sitekey } } = @arrayA;
}
else {
    %{ $sets{ $fasta_id }[ $setscounter ] } = ();
}