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

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

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

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

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

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

...
                my $upperlimit = $span + $lowerlimit;

                for my $sitekey (  @sortedKeys ) {

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for my $hit ( @{ $matches{ $fasta_id }{ $sitekey } } ) {
     next unless $hit >= $lowerlimit;
...
else {
    %{ $sets{ $fasta_id }[ $setscounter ] } = ();
}

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@{ $sets{ $fasta_id }[ $setscounter ]{ $sitekey } } = grep {
    $_ >= $lowerlimit and $_ <= $upperlimit
...
    undef $sets{ $fasta_id }[ $setscounter ] };
    next WEEDLOW;
}

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

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 undef $sets{ $fasta_id }[ $setscounter ] };

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

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```
push @newfast, $h;
```

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

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        for my $checkhash ( keys %{ $sets{ $fasta_id }[ $setscounter ]
+ } ) {
            unless( defined $sets{ $fasta_id }[ $setscounter ]{ $check
+hash }[ 0 ] ) {
...
if( @{ $sets{ $fasta_id } } ) {
    pop @{ $sets{ $fasta_id } } unless scalar %{ $sets{ $fasta_id }[ $
+#{ $sets{ $fasta_id } } ] };
}

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

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