Secondary structures predicted for a fragment of the 3′ region of segment 7 (+)RNA. The top structure is for the hairpin predicted by RNAalifold on the SSCU alignment, while the alternative pseudoknot conformation is shown below. Figure annotations and base pair counts are as described in Figure 5. The predicted free energy of folding, ΔG37° (Mathews et al. 2004), for the consensus hairpin is −14.3 kcal/mol. Predicted free energies for the pseudoknot were calculated as −7 (DP) or −4 (CC) kcal/mol, depending on the parameters used (Dirks and Pierce 2003; Cao and Chen 2006). A slipped helix with G691–C700 and A692–U699 pairs results in a more favorable predicted free energy range of −12 (DP) to −9 (CC), but less favorable percentage of canonical pairing of 79.4% and 89.2%, respectively, for these base pairs.
