use Data::Dumper;  # add this near the top of your script:

# ... now, down at line 383 (had been 382 before adding "use Data::Dumper":
       SITEKEY: for $sitekey (sort {$a <=> $b } keys %{$matches{$fastaseq}}) {
         print "\$matches{$fastaseq}{$sitekey} is:\n",
               Dumper( $matches{$fastaseq}{$sitekey} ); # add this
         SET: foreach $hit ( ... ) {
           # the above print statement used to be here