RNAalifold predicted secondary structure from the RNAz alignment for fragment of 5′ predicted secondary structure region from segment 8 (+)RNA. This structure was also predicted by Ilyinskii et al. (2009). Base pairs are color annotated with information from base pair counts (tabulated to the right of the structure) from an alignment of all available unique sequences. The color annotation key is given below the table. Pairing type is given at the top of the table; canonical pairs to the left, and noncanonical to the right. The “%can” column gives the percentage of canonical pairs found in those aligned positions. Italicized alignment positions (i–j) are for symmetric internal loop bases. The average percent conservation of the whole structure is given below the table. Base pair counts for all unique sequences and cluster b sequences are given without and with parenthesis, respectively. Cluster b consensus sequence is indicated by light blue nucleotides. The predicted free energies of folding, ΔG37° (Mathews et al. 2004), for the consensus sequence of all unique sequences is −19.7 kcal/mol and for cluster b sequences is −8.6 kcal/mol. Nucleotide composition by alignment position is summarized at the bottom of the figure. The structure is notated in bracket notion, codon position is indicated by roman numerals, and consensus amino acid sequence is notated at the top of the table. The percent conservation for each position is also given.
