foreach my $id (keys %hash1){ # you can use (sort keys %hash1) if you want them in a specified order
   if ( exists $hash2{$id} ){
      print "\'$id\' exists in both hashes.\n";
      if ( $hash1{$id} eq $hash2{$id} ){
         ## id and sequence are stored as key value pairs
         print "and the sequences match too.\n";
      }
      else{
         print "but the sequences do not match.\n";
      }
   }
   else {
      print "\'$id\' only exists in hash1.\n";
}

}