Set maximum cutoff score 25
Weakened the prior for non-basepairing nts

Non-basepairing nts have a 4x4 interaction matrix with probabilities on
the diagonal only.  If they make a base-phosphate or base-ribose
interaction, the prior distribution is weakened to emphasize the
observed bases.
Do not take logarithms of probabilities
Fix numbering of non-basepairing bases in cluster
Identify non-modeled bases earlier
Try to ignore .pyc files
Remove unused code