Figure 5

Secondary structure conformations at the 3′ splice site of influenza B segment 8. The top structure is the predicted hairpin for the consensus sequence and the corresponding base pair count table. Below is the alternative pseudoknot conformation and base pair count table. These structures were also proposed by Gultyaev et al. [43]. Figure annotations and base pair count table are as described in Figure 2. The predicted folding free energy, ΔG°₃₇, for the consensus sequence: in hairpin conformation is −9.3 kcal/mol using parameters from RNAstructure [54, 55] and in pseudoknot conformation is −6.0 kcal/mol using parameters from Mathews et al. [55] and Cao and Chen [61].