Inter-Alu sequences in the human genome. (A) Length distribution of inter-Alu distances between two adjacent Alu-transposons in the reference human genome. Heights of bars represent number of adjacent Alu pairs in the human genome at different inter-Alu distances. Subtraction of empty column at < 200 bp representing short inter-Alu sequences that were removed from analysis during library construction for next generation sequencing leaves the solid columns of inter-Alu sequences of varying lengths capturable from the genome. The total sum of the solid columns up to an inter-Alu distance of 6 kb, 8 kb or 10 kb equals 1.10 Gb, 1.36 Gb or 1.58 Gb, respectively. (B) Inter-Alu sequences of 0.2-6.0 kb in length that are in principle capturable by the three Alu-consensual primers AluY278T18, AluY66H21 and R12A/267. Such capturable amplicons amount to ~14 Mb if no mismatch is allowed between the consensual primers and template sequences, or ~106 Mb if one mismatch is allowed per primer. The graph shows the length distribution of the latter 106 Mb.