my ($span, %matches) = @_;
 my ($site, $fastaseq, $fasta, $sitekey) = '';
 my ($setscounter,$lowerlimit,$upperlimit,$i,$set,$yes,$low,$hit) = 0;
 my %sets = ();

 FASTA: for $fastaseq (keys %matches) {
       $sitekey = '';
       SITEKEY: for $sitekey (sort {$a <=> $b } keys %{$matches{$fastaseq}}) {
         if (@{$matches{$fastaseq}{$sitekey}}) {
          SET: foreach $hit (@{$matches{$fastaseq}{$sitekey}}) {
            print "\$matches{$fastaseq}{$sitekey} is: $matches{$fastaseq}{$sitekey}\n";
            print "\$hit is: ",$hit,"\n";
            print "\$hit is: ",$matches{$fastaseq}{$sitekey}[$hit],"\n";
            if ($hit >= $lowerlimit && $hit <= $upperlimit) { #some code
}}}}}

##</code><code>##

$matches{>LG_XIV}{0} is: ARRAY(0x182bb14)
Use of uninitialized value in print at MyScript line 386.
$hit is: 
$hit is: 6906413
Use of uninitialized value in numeric ge (>=) at MyScript line 388.