Fig. 9

a Exact sequence logo determined by RNAsampleCDS for all 2.55×10¹⁷ sequences, whose initial 39 nucleotides code amino acids having BLOSUM62 +1 similarity to the corresponding amino acids from each of the three reading frames in the triple overlapping coding region 344-383 of the reference HCV genome, and whose remaining nucleotides code amino acids having BLOSUM62 +1 similarity to the corresponding amino acids from each of the two reading frames in the double overlapping coding region 383-501 of the reference HCV genome. b Sequence logo determined by RNAiFold 2.0 for the more than 11 million sequences that fold into the HCV FSS structure depicted in Fig. 8, whose initial 39 nucleotides code BLOSUM62 +1 amino acids having BLOSUM62 +1 similarity to the corresponding amino acids from each of the three reading frames in the triple overlapping coding region 344-383 of the reference HCV genome, and whose remaining nucleotides code amino acids having BLOSUM62 +1 similarity to the corresponding amino acids from each of the two reading frames in the double overlapping coding region 383-501 of the reference HCV genome. c Total variation distance shown for each nucleotide position, determined by computing the total variation distance between the position-specific profiles of (a) and (b)