Figure 4.

In(2L)Cy was likely created by ectopic recombination between two foldback transposable elements. A. The distal In(2L)Cy breakpoint (A|B) lies in the 3′ UTR of GlyP and proximal breakpoint (C|D) lies between CG5776 and spict. Reference genome coordinates are shown. B. The general structure of the breakpoint-associated FB insertions. Both insertions have end sequences, spacer sequences and blocks of repeats in mirrored orientations flanking a middle region. Each block contains a single copy of five distinct short repeats, blocks are repeated tandemly a variable number of times, and each block terminates with a CTC motif. An additional 23 bp may be appended to a consensus end sequence. C. The distal (A|C) end of In(2L)Cy includes 2,418 bp of FB sequences, which contain an alternative end sequence and clusters of two and seven repeat blocks, but lack one spacer sequence. Consistent with a recombinant origin, the FB sequences are flanked by a 9 bp tandem site duplication from FB transposition into GlyP (shown as “A”) and another from FB transposition into the CG5776–spict region (“B”). D. The proximal (B|D) end includes 2,563 bp of FB sequences including two spacer sequences and clusters of two and eight repeat blocks. These FB sequences are flanked by the 9 bp duplicated sequences from FB transposition into GlyP (“A”) and the CG5776–spict region (“B”) expected for inversion via ectopic recombination. E. In(2L)Cy arose by recombination between progenitor FB insertions. The high similarity of the FB sequences at the In(2L)Cy ends and the presence of an alternative end sequence at the distal In(2L)Cy end suggests that an FB element within GlyP transposed to the CG5776–spict region and subsequently recombined with an FB element at the donor site.