Fig. 5.

Secondary structural analysis of avian picornavirus 3′-NTRs. a Map of the 3′-NTRs and their relative sizes. The gray box indicates the region aligned by secondary structure predictions in b and c. b The secondary structure alignment of CHK 148 and TRK 22 3′-NTRs (terminal 240 nt), the predicted stem-loop structure (below right), and derived thermodynamic and statistical values for the proposed structure (∆g, avg covariation, avg bp probability and canonical bp). The structure shown was predicted by RNAForester using the Webserver for Aligning non-structural RNAs (WAR, http://genome.ku.dk/resources/war/). c The alignment based on structural prediction for the 3′-NTRs of CHK168, TRK 24, Aichi virus, and Turdivirus, the predicted stem-loop structure (bottom right) and values generated in the derivation of this structure (bottom left). Structural alignments were generated using the IUPAC nucleotide ambiguity system. Boxed sequences in alignments b and c correlate with the boxed loops in the secondary structure predications and are provided for reference and orientation