FIGURE 6.
Alternative secondary structure for the region shown in Figure 5. This was predicted by RNAalifold using the SSCU alignment of segment 8 sequences. Figure annotations and base pair counts are as described in Figure 5. Base pair counts for all unique sequences and cluster b sequences are given without and with parentheses, 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 −9.6 kcal/mol and for cluster b sequences is −23.8 kcal/mol.
