FIGURE 4.

The CRE region. Sequence and secondary structure of the HCV CRE region, including the functional domains 5BSL3.1, 5BSL3.2, and 5BSL3.3 plus the 5BSL3.4 stem-loop. Conserved residues and covariant base pairs in the essential 5BSL3.2 domain, as described by You et al. (2004), are indicated in boxes. Colors denote the frequency for each nucleotide variation, as indicated. NP (non-paired) represents nucleotide variations impeding the formation of canonical base pairs. The translation stop codon is indicated in enlarged blue letters. Position numbering is as in Figure 2.