Table 2.
Percentage of Bases of LINE-1 Subfamilies That Match piRNAs
| LINE-1 Subfamily | Number of Bases in LINE-1s | 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), % |
| LINE-1 HS (human specific) | 3,458,046 | 15.96 | 11.87 | 4.23 |
| LINE-1 PA2 (7.6 Ma) | 9,493,804 | 16.56 | 11.35 | 3.83 |
| LINE-1 PA3 (12.5 Ma) | 18,923,178 | 12.71 | 8.91 | 3.23 |
| LINE-1 PA4 (18.0 Ma) | 18,340,583 | 11.18 | 7.17 | 2.23 |
| LINE-1 PA5 (20.4 Ma) | 15,765,637 | 11.55 | 6.92 | 1.64 |
| LINE-1 PA6 (26.8 Ma) | 10,819,404 | 9.26 | 5.90 | 1.48 |
| LINE-1 PA7 (31.4 Ma) | 19,129,677 | 6.14 | 3.55 | 0.96 |
| LINE-1 PA8 (40.9 Ma) | 6,561,140 | 7.06 | 4.23 | 1.00 |
| LINE-1 (all) | 504,651,578 | 3.09 | 1.63 | 0.37 |
Note.—All LINE-1 subfamilies annotated in RepeatMasker (http://www.repeatmasker.org) are listed from youngest to oldest (top to bottom). The age of each LINE-1 subfamily was taken from Khan et al. (2006). 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). There is a strong correlation between the age of the subfamily and the percentage of bases that match piRNAs.