Hmm, that looks like it would match fine. But I don't see how it would limit a string to containing any number of occurances of only two of the alternate codes?

In case I wasn't clear in my first posting, the regex should match on a string that is within the QC criteria, but fail if not. So:

ATCGGTATATATRGTCGAYGCRGTCAGA

Would be matched, but:

ATCGGTATATATRGTCGAYGCNGTCAGA

Wouldn't, because the N near the end introduces a third ambiguity code.