> I speculated that this poor performance might be caused by the newline bytes (0x0A) punctuating every 60 characters of sequence, breaking the hashes used for long range pattern matching.

If the linefeeds were treated as semantic characters and not allowed to break the hash size, you would get similar results without pre-filtering and post-filtering. It occurs to me that this strategy is so obvious that there must be some reason it won't work.