Figure 2.

Consensus secondary structure of the 5′ TR/3′ TR long-range interaction, computed from a structural multiple sequence alignment of 20 mosquito-borne flaviviruses (Supplementary Figure S1). Coloring of base pairs follows the RNAalifold schema and indicates different covariation levels, ranging from red (no covariation, full primary sequence conservation) to violet (full covariation, all six possible combinations of base pairs) at corresponding columns of the underlying alignment. The duplex formed by the almost fully sequence-conserved 11 nt cyclization sequences (highlighted in gray) represents the only long-range interaction in the consensus structure. Canonical 5’TR elements (SLA, SLB, and cHP), as well as 3’TR elements (DB, sHP and 3’SL) are predicted to fold in the consensus structure, indicating that they are energetically more favorable than an extended long-range interaction duplex structure.