John Parsch Last revised Feb.
Usage is fairly self-explanatory.
Sequence 2 should be a reverse complement if you are searching for RNA stems. The observed pairing score is compared to a random distribution of scores generated by finding stems between random permutations of sequences 1 and 2. You may choose to randomize seq. 2, or both. You may also choose to do the randomizations in non-overlapping windows of 10 or more bases.