Figure 1.

Example parse tree for pairSCFG. Panel A shows an example parse tree for the pairSCFG described in the text. The grammar emits two correlated sequences, x (above, in black) and y (below, in blue). The individual structures are shown in Panel B. The resulting structural alignment is shown in Panel C, with lines connecting base pairs in each sequence. The annotation string is shown between sequence x and y (see Appendix for details). Note that the structure for x (above, in black) has what is most likely an unconserved base pair C·G in the second stem of the structure.