FASTA: for (my $h=0;$h<(@fastarray);$h++) {
  $setscounter = 0;
  if (defined %{$matches{$fastarray[$h]}}){
   SITE: for $site (sort {$a <=> $b } keys %{$matches{$fastarray[$h]}}) {
    if (@{$matches{$fastarray[$h]}{$site}}) {
     $i = 0;
     ELEM: while ($i < length(@{$matches{$fastarray[$h]}{$site}})) {
       $lowerlimit = 0;
       my $low = $matches{$fastarray[$h]}{$site}[$i];
       $lowerlimit = $low + 0;
       $upperlimit = $span + $lowerlimit;
       SITEKEY: for $sitekey (sort {$a <=> $b } keys %{$matches{$fastarray[$h]}}) {
         if (@{$matches{$fastarray[$h]}{$sitekey}}) {
          my @arrayA = ();
          my $hit = 0;
          SET: while ($hit < length(@{$matches{$fastarray[$h]}{$sitekey}} )) {
            print "...in \$matches{$fastarray[$h]}{$sitekey}[$hit]\n";
            if ($matches{$fastarray[$h]}{$sitekey}[$hit] >= $lowerlimit && $matches{$fastarray[$h]}{$sitekey}[$hit] <= $upperlimit) {
              push (@arrayA, $matches{$fastarray[$h]}{$sitekey}[$hit]);
              $hit++;
              next SET;
              #closes If setcount
              }
              elsif ($matches{$fastarray[$h]}{$sitekey}[$hit] < $lowerlimit) {
                $hit++;
                next SET;
                }
              else {$hit++;}
            #closes while hit
            }
          if (@arrayA && $hit == length(@{$matches{$fastarray[$h]}{$sitekey}})) {
            $sets{$fastarray[$h]}[$setscounter]{$sitekey} = \@arrayA;
            print "\$sets{$fastarray[$h]}[$setscounter] is:\n";
            print Dumper(%{$sets{$fastarray[$h]}[$setscounter]}); 
            @arrayA = ();
            }
            else {
              $sets{$fastarray[$h]}[$setscounter]{$sitekey} = undef;
              }
          $hit = 0;
          next SITEKEY; 
          #closes if matches
          }
         next SITEKEY;  
         #closes SITEKEY  
         } 
       $setscounter++;
       $i++;   
       next ELEM;
       # closes while i
       }
     #closes if matches
     }
     next SITE;
    #closes for my site
    }
   #closes if defined
   }
   next FASTA;
   #closes for fastarray
  }

##</code><code>##

...in $matches{>scaffold_446}{0}[1]
$sets{>scaffold_446}[1] is:
$VAR1 = '0';
$VAR2 = [
          0,        #  These 2 array elements should not BOTH 
          0         #  be 0!!!  What did I do wrong?
        ];
...in $matches{>scaffold_446}{1}[0]
...in $matches{>scaffold_446}{2}[0]
...in $matches{>scaffold_446}{0}[0]
...in $matches{>scaffold_446}{0}[1]
...in $matches{>scaffold_446}{1}[0]
$sets{>scaffold_446}[2] is:
$VAR1 = '1';     #  For each of these different  '...in $matches..."
$VAR2 = [        #  There should be 6 $VAR variables.  corresponding 
          40048    #  to 3 key/value pairs, but I am doing something wrong
        ];              #  in my code, such that sometimes there are 3 pairs, but
$VAR3 = '0';     #  often not.  Any thoughts?
$VAR4 = undef;
...in $matches{>scaffold_446}{2}[0]
...in $matches{>scaffold_446}{0}[0]
...in $matches{>scaffold_446}{0}[1]
...in $matches{>scaffold_446}{1}[0]
...in $matches{>scaffold_446}{2}[0]
$sets{>scaffold_446}[3] is:
$VAR1 = '1';
$VAR2 = undef;
$VAR3 = '0';
$VAR4 = undef;
$VAR5 = '2';
$VAR6 = [
          5468
        ];
...in $matches{>scaffold_3198}{0}[0]
$sets{>scaffold_3198}[0] is:
$VAR1 = '0';
$VAR2 = [
          1829
        ];