Figure 2
Secondary structure predicted for the consensus sequence at the 5′ splice site of influenza B segment 8. Base pair counts from an alignment of all available unique sequences are tabulated to the right of the structure. Base pairing positions (i-j) and types are given in the table with canonical pairs to the left and non-canonical pairs to the right. “%can” column represents the percentage of canonical pairs found at each i-j position in the alignment and the average percent conservation of the structure is given below the column. The italicized alignment positions (i-j) indicate possible non-canonical base pairing interactions in loop regions predicted with MC-Fold [58]. Mutations from canonical to canonical base pairs are in green and from canonical to non-canonical base pairs are in orange. The mutations are also annotated on the structure. The red arrow in the structure indicates the splice site and the dashed lines indicate possible non-canonical base pairing interactions in loop regions predicted with MC-Fold [58]. The predicted folding free energy, ΔG°37, for the consensus hairpin is −12.5 kcal/mol using parameters from RNA structure [54, 55].