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Expected variation between Alu alignment divergences. To assess the expected divergence between any two Alu alignments within the analyzed 2,366 duplications, we computed all pairwise differences for the internal (control) Alus within a segmental duplication alignment (KinternalAlu1-KinternalAlu2) (see the “Material and Methods” section). A total of 5,306 comparisons were analyzed. The SD was 0.031.
