Identification of potential conserved RNA secondary structure throughout influenza A coding regions

Secondary structure models for fragment of 3′ predicted secondary structure region from segment 8 (+)RNA. The top structure is for the hairpin predicted by RNAalifold on the SSCU alignment, while the alternative pseudoknot conformation is shown below. These structures were also predicted by Gultyaev et al. (2007). 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 −18.9 kcal/mol. Predicted free energies for the pseudoknot were calculated as −9 kcal/mol (Dirks and Pierce 2003; Cao and Chen 2009).