Figure 1. Base‐pair probability plot. The larger dots represent higher probabilities. Probable stems can be identified as diagonals of the large dots. Two structures are shown at the bottom in dot‐bracket notation. Single‐stranded regions can be identified as blocks “reflected” at the main diagonal that contain no probable base pairs.

Figure 2. Example analysis.   (a) Base‐pair probability plot (see Section 53.2.2.1). Larger single‐stranded regions were highlighted. The two PTB‐bindingsites (red) [ 14] are found in these regions. The plot also indicates that the exon and 3′ splice site are sequestered in a stem;   (b) PU value plots (see Sections 53.2.2.2 or 53.2.3.2, using hexamers and context lengths 11–30 nt) show that the upstream PTB site (CTCTCT, yellow) is rather single‐stranded (top). Mutating this site to CTGGGT (middle) likely leads to structural changes and decreases the single‐strandedness of this motif, while a mutation to CTAAAT (bottom) does not change the predicted structure.