That doesn't solve the any number of no more than two different characters part. Both solutions posted so far will match up to 2 non-atcg characters, but I read the spec as allowing for, say 50 Rs and 100 Ws to be mixed in, but not one each of Y, H, and N.

I could be wrong, but I have a feeling that this one can't be solved by a single regex. (Or at least not one written by a mere mortal - there are some regex deities floating around here who might prove me wrong...)