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Covariant bases involved in long-range interactions between the IRES and the 3΄UTR. The pattern of nucleotide conservation (measured in bits) of the IRES and the 3΄UTR predicted to interact by TRANSAT is represented by a sequence logo obtained from the sequence alignment of FMDV field isolates. The IRES domains (4 or 5) and the 3΄UTR stem-loops (SL1, H and SL2) and the nucleotide positions for each interacting region are indicated. A dash denotes canonical base pairs.
