for my $site ( sort { $a <=> $b } keys %{ $matches{ $fasta_id } } ) {  ## A
    last unless @{ $matches{ $fasta_id }{ $site } };

    WEEDLOW: for my $low ( @{ $matches{ $fasta_id }{ $site } } ) {
        my $lowerlimit = $low + 0;
        my $upperlimit = $span + $lowerlimit;

        for my $sitekey ( sort { $a <=> $b } keys %{ $matches{ $fasta_id } } ) { ## B