Long-range interactions in 5′ UTR, CRE, VR, and X-tail. (A) Overview. (Gray) Known interactions (No. 13–17 from the literature, validated by our analysis for all examined isolates); (green) new interactions (from our calculations). Numbers indicate different interactions shown in detail in B. (B) Interactions for all available sequences labeled with numbers corresponding to A. Bottom numbers indicate number of sequences in the alignment used for the interaction. Interaction No. 1 can be extended for a possible circularization. (C) Possible circularization of the HCV RNA. The interaction of SLII and DLS of HCV plus-strand RNA can be extended to at least 62 bp in all available 19 isolates. (D) Corresponding interaction of minus-strand RNA.
