Wrong about RALEE bug

After having email discussion with Sam Griffiths-Jones, the author of RALEE, I discovered that there was a difference interpretation, not a bug, and I decided that Sam's interpretation was better.

I had interpreted a contiguous run of base pairs to be a helix, but after looking at a few structures in VARNA, I realized that some of the "helices" could be considered one helix with a few bulges. Sam gave some good examples:

You have continuous on one side, but not the other:

.((((((...))).))).

Alignments where a helix is continuous in most sequences, but bulged occasionally:

AGCGCUUCG.CU
AGCGCUUCG.UU
AGCGCCGCG.CU
AGCGCUUCG.CU
AGGGCUUCC.CU
AGCGCUUCGGCU
((((...)).))

In the above case, what is a helix could be subject to arbitrary change, just by adding one sequence with a bulge.