Thanks very much for the explanation, I do understand it! I don't have much time right now to look at it more deeply, but I do have two more questions about the sample data you showed in the OP: What is the first column? You mentioned something about "the most energy stable hairpin", is this related and could you use the first column to select the hairpin?

Second, do I understand correctly that the first ~13 lines of sample data in the OP contain what looks like four different hairpins? Do you need to select one out of each of the four? Or, if not and you only need to choose a single hairpin out of all of that data, by what criteria do you choose which one?