If your two sequences are always the exact same length and you simply want to compare equivalent positions (I think I'm understanding that correctly), you may want to simply store each sequence each as their own simple scalar string and make use of the substr function for comparison of positions. That way you could query the position alone and have it return which protein is in that position in both strings.

Admittedly, I could be oversimplifying the problem if I've misunderstood.