Figure 1. Nucleotide Similarities within HCV 5′- and 3′-Genome Ends

Top panel: schematic representation of the HCV reference genome H77 as given in the 2008 LANL database.

Bottom panel: Percent nucleotide identity along the 5′-NCR and the X-tail, as calculated by a sliding window analysis with VectorNTI software. Window size was 2 nucleotides. The alignment used for the sliding window analysis contained the complete HCV genotype reference panel (n = 60 sequences) from the LANL HCV database (available at http://hcv.lanl.gov/content/sequence/NEWALIGN/align.html) and all X-tail sequences available in GenBank as shown in Text S2, including the sequences determined de novo in this study (EU835523-EU835532).