Figure 3

FAP I:D ratio versus Alu pair sequence number. The APSN, with (red) and without (blue) correction for CLIQUEs. (A) The I:D ratio of full length Alu pairs for APSNs of ± 1,000 Alu elements. Note that a bubble of depressed I:D ratio exists for those elements within about ± 100 Alu elements of the central Alu element. (B) A closer view of the I:D imbalance bubble. The 95% confidence for each value is estimated ± 0.6%. Therefore, the bubble of I:D imbalance extends for an approximately APSN = ± 85 around the central Alu. A more rigorous treatment of the data (see text) extends this I:D imbalance boundary to an APSN = ± 107. (C) Over 99% of the impact of CLIQUEs on the FAP I:D ratio dissipates after the APSN = 5. The largest CLIQUEs, while rare, contain up to 32 Alu elements. No CLIQUE impact exists on the FAP I:D ratio for an APSN > 31. APSN: Alu pair sequence number; CLIQUE: catenated LINE1 endonuclease induced queue of uninterrupted Alu, LINE1 and SVA elements; FAP: full-length Alu pair; I:D Ratio: ratio between inverted and direct Alu pairs.