I'm trying to find out the structure of a conserved ITS loop. As my initial prediction (using only bases homologous to those present in the loop in a closely-related species) was fairly low-scoring, I toyed around with the edges until it significantly improved.
For this I used RNAfold from the Vienna suite. The MFE and centroid predictions are the same, which I read suggests strong support. The frequency of the MFE structure in the ensemble is ~40%. The ensemble diversity is 9.12 (I am not sure how to interpret this last number).
I checked the same RNA sequence with Mfold. This resulted in two similarly-scoring models, the second of which is the RNAfold one. The first one is identical except for the base of the stem of the loop (where instead of having bases paired in a stem, it has two separate single strands, one of which curls in a small hairpin loop.
Is this an example of an RNA structure ensemble? My understanding is that an ensemble is an array of structurally similar, but slightly different RNAs of identical sequences.
Or is one of the models simply wrong? How would I go about figuring that out?