FIG. 5.

(A) Alignment of the minimal size of the 5′TR element of T36 isolate (identified by mutational analysis) with the corresponding region of other isolates of CTV. The GenBank accession numbers of the sequences of different CTV isolates are as follows: T36, NC_001661; T30, AF260651; VT, U56902; T385, Y18420; SY568, AF001623; and NUagA, AB046398. Only the nucleotide differences from T36 are shown. Hyphens represent the conserved nucleotides in all isolates, and the gaps were introduced for optimal alignment. Positions of the predicted stem-loop 1 (SL1) and stem-loop 2 (SL2) are indicated. (B) The predicted secondary structure of plus (left) and minus (right) strands of the 5′TR element and their respective free energies obtained using the MFOLD program (28). The putative stem-loops (SL1 and SL2) are indicated.