FIG. 3.

The homologous repeat units of TBE (A) and CTE (B) form similar mirror-symmetrical pairs in the secondary structure. The juxtaposed repeats are shown by black and grey arrows in the schematic drawings, and by bold italics in the RNA sequences. Boxes that are aligned to the matching regions of the schematic drawing indicate the mirror-symmetrical pairs of repeats. The internal loops A and B and the hairpin loop of CTE are indicated. The secondary structures are shown for the portions of the CTE from SRV-1 (38) and of the IAP-related retroelement ORG-IAP (37), as indicated to the right. For TBE, a portion of the secondary structure model is shown, and its regions are marked as indicated for Fig. 2.