$hash{$Query}[3] = $one;
           $hash{$Query}[4] = $two;

##</code><code>##

while (<FH>) {
   my ($Query, $Score, $Start, $End, $one, $two) = split;
   my $aref=[$Score, $Start, $End, $one, $two];

   if ( ! exists ( $hash{$Query} ) ) {
      $hash{$Query} = $aref;
   }
   else {
      if ( $hash{$Query}[1] > $Start ) {
           $hash{$Query} = $aref;
      }
   }
   if ( ! exists ( $hash2{$Query} ) ) {
      $hash2{$Query}= $aref;
   }
   else {
      if ( $hash2{$Query}[2] < $End ) {
           $hash2{$Query} = $aref;
      }
   }
}