(A) Alu-mediated NAHR and preferential attachment are two complementary mechanisms for SD formation. In Alu-rich regions (>10 Alu elements per 10 kb), the association of SDs and pre-existing SDs is much lower than in Alu-poor regions (no Alu elements per 100 kb). Associations are given as Spearman rank correlations of the number of occurrences in genomic bins. All correlations are highly significant (P-value ≪ 0.00001). (B) Association of Alu elements and SDs is highest for the oldest (∼40 Mya) SDs and drops significantly for recent SDs. At the same time, preference for subtelomeric regions and a presumed NHEJ mechanism rises. Associations are given as Spearman rank correlations of the number of occurrences in genomic bins. All correlations are highly significant (P-value ≪ 0.00001).
