And how do you represent an unknown base in that representation? Or, how would you do the comparison with a gap in one of the sequences (which is incredibly com

And how do you represent an unknown base in that representation? Or, how would you do the comparison with a gap in one of the sequences (which is incredibly common). I've benchmarked it all too, and it is really difficult to represent DNA with just two bits. Once you start to get out from the simplest use-cases, it gets significantly more difficult. The most efficient mechanisms require three bits or at least some mechanism for denoting where the ambiguous calls are (see UCSC's 2-bit format). And now that you're dealing with three bits, the numbers start to get funky quickly - you end up dealing with 24 bits for 6 consecutive bases, and you still have the problem of representing gaps efficiently... have you ever tried to insert 4 bits in the middle of another number?