FIG. 4.

Alignment of the duplicated region of 19 YF-XL isolates, genomic positions 10533 to 10749 (3′ NCR 182 to 398; Asibi reference numbering). Sequences shown in red are the downstream duplicates of the sequences shown in black. Multiple isolates with 100% identity are represented by a single sequence. Regions involved in basepairing are boxed and labeled to correspond to stem structures as indicated in Fig. 1A and 2A. Hatched boxes indicate pseudoknot binding sites; red boxes indicate conserved substitutions among duplicated structures.