Full length and 5' truncated junctions of the Drosophila R1 insertions. Shown at the top is the sequence of the 28S gene insertion site. Various regions of the sequence have been indicated with colors to allow the 5' and 3' junctions of the R1 insertions to be summarized. Position +1 corresponds to the position of bottom-strand cleavage based on the 3' junctions of all R1 elements as well as from in vitro studies of the R1 endonuclease [12, 13]. Positions -9 and +14 correspond to the inferred most frequent sites of top-strand cleavage. Shown at the bottom are diagrams of the 5' and 3' junctions of R1 insertions. Full-length as well as 5' truncated insertions of the ancestral type R1s have 14 bp target site duplications (left side). The bracketed region of the junctions exhibited sequence variation. This variation can correspond to non-templated nucleotides (sequences corresponding to neither the 28S gene nor the R1 element), or microhomologies (1 to 5 nucleotides that could correspond to either the 28S gene or the R1 element). Melanogaster group R1s have three classes of junctions (right side): full length insertions with a precise 9 bp target site deletion; full length insertions with an insertion site rearrangement (ISR); and 5' truncated insertions. Sequence variation at these junctions is limited to the bracketed region and corresponds to the variation seen in the ancestral type R1s. The tables at the bottom show the fraction of copies observed at the bracketed site that are precise, contain non-templated nucleotides (extra nt) or microhomologies (micro).