WEEDLOW: for my $low ( @{ $matchesfasta_id{ $site } } ) {

##</code><code>##

     last unless @{$matches{$fasta_id}{$site}};

##</code><code>##

            WEEDLOW: for my $low (  @{ $matches{ $fasta_id }{ $site } }) {

##</code><code>##

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

##</code><code>##

        my @sortedKeys = sort { $a <=> $b } keys %{ $matches{ $fasta_id } };

        for my $site ( @sortedKeys ) {
            last unless @{ $matches{ $fasta_id }{ $site } };

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

                for my $sitekey (  @sortedKeys ) {

##</code><code>##

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 ] } = ();
}

##</code><code>##

@{ $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;
}

##</code><code>##

%{ $sets{ $fasta_id }[ $setscounter ] } = ();

##</code><code>##

 undef $sets{ $fasta_id }[ $setscounter ] };
 
##</code><code>##

#   @fastarray = ();
@fastarray = @newfast;

##</code><code>##

push @newfast, $h;

##</code><code>##

if( scalar keys %{ $sets{ $fasta_id }[ $setscounter ] } < $num ) {

##</code><code>##

        for my $checkhash ( keys %{ $sets{ $fasta_id }[ $setscounter ] } ) {
            unless( defined $sets{ $fasta_id }[ $setscounter ]{ $checkhash }[ 0 ] ) {
                undef $sets{ $fasta_id }[ $setscounter ] };
                last;
            }
        }
        if( scalar keys %{ $sets{ $fasta_id }[ $setscounter ] } < $num ) {
            undef $sets{ $fasta_id }[ $setscounter ];
        }
        $setscounter++ if scalar %{ $sets{ $fasta_id }[ $setscounter ] };
    }
}
if( @{ $sets{ $fasta_id } } ) {
    pop @{ $sets{ $fasta_id } } unless scalar %{ $sets{ $fasta_id }[ $#{ $sets{ $fasta_id } } ] };
}

##</code><code>##

sub WEED {
    my( $span, %matches) = @_;
    my( $site, $fasta, $sitekey) = '';
    my( $setscounter, $lowerlimit, $upperlimit, $i, $set, $yes ) = 0;
    my %sets = ();
    my @newfast;

    for my $fasta_id ( @fastheaders ) {
        $setscounter = 0;
        next unless defined %{ $matches{ $fasta_id } };
        print "Currently analysing results from sequence:\n     $fasta_id\n";

        for $site ( sort { $a <=> $b } keys %{ $matches{ $fasta_id } } ) {
            last unless @{ $matches{ $fasta_id }{ $site } };
            $i = 0;
            WEEDLOW: for my $low ( @{ $matches{ $fasta_id }{ $site } } ) {
                $lowerlimit = $low + 0;
                $upperlimit = $span + $lowerlimit;
                for $sitekey ( sort { $a <=> $b } keys %{ $matches{ $fasta_id } } ) {
                    next unless defined @{ $matches{ $fasta_id }{ $sitekey } };
                    my @arrayA = ();
                    for my $hit ( @{ $matches{ $fasta_id }{ $sitekey } } ) {
                        next unless $hit >= $lowerlimit;
                        last unless $hit <= $upperlimit;
                        my $ggg = $hit + 0;
                        push( @arrayA, $ggg);
                        $ggg = 0;
                        next;
                    }
                    if( @arrayA ) {
                        @{ $sets{ $fasta_id }[ $setscounter ]{ $sitekey } } = @arrayA;
                        @arrayA = ();
                    }
                    else {
                        %{ $sets{ $fasta_id }[ $setscounter ] } = ();
                        next WEEDLOW;
                    }
                }
                for my $checkhash ( keys %{ $sets{ $fasta_id }[ $setscounter ] } ) {
                    unless( defined $sets{ $fasta_id }[ $setscounter ]{ $checkhash }[ 0 ] ) {
                        %{ $sets{ $fasta_id }[ $setscounter ] } = ();
                        last;
                    }
                }
                if( scalar keys %{ $sets{ $fasta_id }[ $setscounter ] } < $num ) {
                    %{ $sets{ $fasta_id }[ $setscounter ] } = ();
                }
                $setscounter++ if scalar %{ $sets{ $fasta_id }[ $setscounter ] };
            }
        }
        if( @{ $sets{ $fasta_id } } ) {
            pop @{ $sets{ $fasta_id } } unless scalar %{ $sets{ $fasta_id }[ $#{ $sets{ $fasta_id } } ] };
        }
        if( @{ $sets{ $fasta_id } } ) {
            push @newfast, $h;
        }
        else {
            delete $sets{ $fasta_id };
        }
    }
    @fastarray = ();
    @fastarray = @newfast;
    return %sets;
}

##</code><code>##

sub WEED {
    my( $span, %matches) = @_;
    my %sets;
    my @newfast;

    for my $fasta_id ( @fastheaders ) {
        my $setscounter = 0;
        next unless defined %{ $matches{ $fasta_id } };
        print "Currently analysing results from sequence:\n     $fasta_id\n";
        my @sortedKeys = sort { $a <=> $b } keys %{ $matches{ $fasta_id } };

        for my $site ( @sortedKeys ) {
            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 (  @sortedKeys ) {
                    next unless defined @{ $matches{ $fasta_id }{ $sitekey } };
                    @{ $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;
                    }
                }
                for my $checkhash ( keys %{ $sets{ $fasta_id }[ $setscounter ] } ) {
                    unless( defined $sets{ $fasta_id }[ $setscounter ]{ $checkhash }[ 0 ] ) {
                        undef $sets{ $fasta_id }[ $setscounter ] };
                        last;
                    }
                }
                if( scalar keys %{ $sets{ $fasta_id }[ $setscounter ] } < $num ) {
                    undef $sets{ $fasta_id }[ $setscounter ];
                }
                $setscounter++ if scalar %{ $sets{ $fasta_id }[ $setscounter ] };
            }
        }
        if( @{ $sets{ $fasta_id } } ) {
            pop @{ $sets{ $fasta_id } } unless scalar %{ $sets{ $fasta_id }[ $#{ $sets{ $fasta_id } } ] };
        }
        if( @{ $sets{ $fasta_id } } ) {
            push @newfast, $h;
        }
        else {
            delete $sets{ $fasta_id };
        }
    }
    @fastarray = @newfast;
    return %sets;
}