FIG. 2.

5′ junctions of full-length R2 elements. Sequences were derived by PCR from several D. simulans stocks shown in Fig. 1 (34, 58, and 89) or obtained from the GenBank trace archives of the D. simulans genome. Shaded boxes indicate the sequences corresponding to the upstream 28S gene or the R2 element. Nucleotides added during the retrotransposition process are shown in the middle unshaded region. Many of the full-length R2 junctions in the D. simulans stocks studied here are identical and define the standard (most common) junction (top sequence). All other junctions are present at low frequencies. To the right of each sequence is indicated the difference in length, compared to the standard junction length, of PCR or RT-PCR products in assays similar to those represented in Fig. 1C. #, the junction used as construct b in Fig. 3. *, the junction tested for self-cleavage in Fig. 5.