FIGURE 4.

Nucleotide alignment of the frameshift region in Sireviruses. (A) The first 31 columns in the alignment are highly conserved, self-complementary, and predicted to fold into a stem–loop structure. For the maize retrotransposons, covariant changes that preserve self-complimentary are marked by the arrows. The asterisk indicates the stop codon in gag. The diamond indicates the position of the stop codon in pol. The boxes mark the occurrence of the gag and the pol stop codons. (B) The stem–loop structure of the conserved motif.