Table 3.

Percentage of Bases of Alu Subfamilies That Match piRNAs

Alu Subfamily	Number of Bases in Alu Subfamily	Percentage of Bases Matching piRNAs (1 mismatch, 1 indel), %	Percentage of Bases Matching piRNAs (1 mismatch, 0 indel), %	Percentage of Bases Matching piRNAs (0 mismatch, 0 indel), %
AluYg6 (2 Ma)	162,316	33.99	21.86	13.86
AluYb9 (5 Ma)	9,126,467	41.17	20.77	17.29
AluYb8 (5–15 Ma)	8,802,284	50.87	31.30	20.23
AluYa5 (5–15 Ma)	1,168,599	30.46	19.92	17.66
AluY (25 Ma)	39,622,226	29.78	17.57	9.05
AluSg (31 Ma)	23,605,918	28.64	15.39	4.70
AluSx (37 Ma)	97,504,435	28.07	14.04	3.69
AluSq (44 Ma)	26,932,423	32.23	18.16	4.97
Alus (all)	307,703,885	27.01	14.35	4.20

Note.—All Alu subfamilies annotated in RepeatMasker (http://www.repeatmasker.org) are listed from youngest to oldest (top to bottom). The age of the Alu subfamilies was compiled from data in Kapitanov and Jurka (1995), Batzer and Deininger (2002), and Salem et al. (2003). The number of bases contained in TEs from each subfamily (column 2) and the percentage of bases that match piRNAs are shown at different matching stringencies (columns 3–5). The bold horizontal lines demarcate major transitions in Alu evolution (Batzer and Deininger 2002). The correlation between the age of the subfamily and the percentage of bases that match piRNAs is discernable across the major groups of Alus. However, within groups, the correlation is weaker than the correlation for LINE-1 elements, perhaps because of the greater uncertainty in the ages of the Alu subfamilies.