Depictions of secondary structures for the L. collosoma Spliced Leader sequence: (A) two-dimensional “airport terminal” diagram of the Minimum Free Energy (MFE) state; (B) classic “rainbow” diagram (MFE); (C) bracket notation with periods representing unpaired bases and parentheses indicating paired bases (MFE). (D) A dot plot with partition function probabilities Pij with base i vertical and base j horizontal. Color is assigned on the basis of the logs of probabilities. (Graphics adapted from RNAstructure.) (E) ViennaRNA’s prediction (using slightly different free energy rules) with bases color-coded according to their partition function probabilities. (Graphics adapted from ViennaRNA.) (F) A Dot Plot available from ViennaRNA uses box-size proportional to probability (top triangle), but the grid obscures low-probability pairs. (G) An AllPairs RNAbow diagram with the line width and darkness proportional to the probability of the base pairs. (H) A Clusters RNAbow diagram after resolving into the two dominant clusters, with probability 0.57 (red) and 0.43 (blue); note that the MFE state (B) belongs to the less-probable blue cluster.
