Figure 3

ITR recombination frequency and structure. (A) Number of unique viral breakpoints recorded for each nucleotide position in the first 120 bases of the ITR; numeral represents distance from the viral 5' end. Colored bars correlate with ITR features as described in panel B. (B) Nucleotide positions and features of the AAV ITR, with numerals indicating distance from 5' viral end. Green represents unassigned activity; red represents the recombination hotspot hairpin; blue denotes the rep binding sites; and orange reflects the Rep nicking site (TRS). (C) The percent of total recombination events involving viral-chromosomal junctions, viral-viral junctions, and mixed junctions, i.e. both viral-viral and viral-chromosomal recombination in the same molecule. (D) The percent of total validated sequences that are intact virus, viral-chromosomal junctions with intact, single-copy virus, and sequences involving viral-viral recombination.