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Table 1 Copy number, length, divergence and age of Perrisodactyla L1 families. The families are organized by promoter types (from 1 to 7)

From: Contrasted patterns of evolution of the LINE-1 retrotransposon in perissodactyls: the history of a LINE-1 extinction

   Divergence and age of families based on their 3′ extremity Genomic Copy # Genomic FL Copy #
Family Name Length of consensus (bp) Average pairwise divergence Average divergence from consensus (% ± S.E.) Age (Myr) Ec Cs Ec Cs
L1_Ec1_I 6639 0.70 ± 0.20 0.43 ± 0.38 2.7 (1.9–3.5) 571 94 (57)
L1_Ec1_II 6644 0.80 ± 0.20 0.46 ± 0.11 3.1 (2.3–3.8) 532 102 (64)
L1_Ec1_III 6539 0.80 ± 0.20 0.43 ± 0.09 3.1 (2.3–3.8) 420 2 (3)
L1_Ec1_IV 6411 1.40 ± 0.20 0.69 ± 0.08 5.4 (4.6–6.2) 1589 147 (77)
L1_Ec1_V 6664 1.80 ± 0.20 1.08 ± 0.19 6.9 (6.2–7.7) 635 117 (73)
L1_Ec1_VI 6716 4.70 ± 0 .40 2.64 ± 0.24 18.1 (16.5–19.6) 630 73 (16)
L1_Ec1_VII 7914 3.30 ± 0.10 1.68 ± 0.08 12.7 (12.3–13.1) 1285 88 (15)
L1_Ec1_VIII 6701 3.60 ± 0.30 2.02 ± 0.19 13.8 (12.7–15.0) 459 37 (17)
L1_Ec1_IX 6787 5.80 ± 0.40 3.16 ± 0.22 22.3 (20.8–23.8) 1931 140 (15)
L1_Ec1_X 6791 11.20 ± 0.50 6.10 ± 0.33 43.1 (41.2–45.0) 3571 251 (53)
L1_Ec2_I 5924 1.00 ± 0.10 .051 ± 0.03 3.8 (3.5–4.2) 2561 403 (31)
L1_Ec2_II 5918 4.40 ± 0.30 2.47 ± 0.21 16.9 (15.8–18.1) 1350 166 (11)
L1_Ec2_III 5943 5.90 ± 0.30 3.22 ± 0.24 22.7 (21.5–23.8) 355 2 (0)
L1_Ec2_IV 5941 5.80 ± 0.30 3.12 ± .021 22.3 (21.2–23.5) 477 58 (5)
L1_Ec2_V 5950 6.00 ± 0 .30 3.20 ± 0.20 23.1 (21.9–24.2) 1423 137 (13)
L1_Ec2_VI 5963 7.70 ± 0 .30 4.13 ± 0.23 29.6 (28.5–30.8) 1839 196 (23)
L1_Ec2_VII 5986 9.60 ± 0.40 5.17 ± 0.28 36.9 (35.4–38.5) 4508 572 (35)
L1_Cs2_I 6002 5.2 ± 0.40 2.9 ± 0.25 20.0 (18.5–21.5) 6700 512 (6)
L1_Cs2_II 5686 8.7 ± 0.40 4.8 ± 0.33 33.5 (31.9–35.0) 2372 140 (4)
L1_Cs2_III 5518 9.5 ± 0.40 4.9 ± 0.24 36.5 (35.0–38.1) 1716 46 (12)
L1_Perissodactyla2_I 6127 13.90 ± 0.40 7.27 ± 0.29 53.5 (51.9–55.0) 9208 6572 476 (78) 312 (6)
L1_Cs3_I 6218 5.8 ± 0.30 3.0 ± 0.16 22.3 (21.2–23.5) 2755 234 (1)
L1_Ec4_I 6997 3.60 ± 0.20 1.95 ± 0.12 13.8 (13.1–14.6) 2622 141 (13)
L1_Ec4_II 6993 8.00 ± 0.40 4.38 ± 0.24 30.8 (29.2–32.3) 4150 316 (40)
L1_Ec4_III 7014 9.90 ± 0.40 5.34 ± 0.26 38.1 (36.5–39.6) 6549 251 (21)
L1_Perissodactyla4_I 7048 11.30 ± 0.40 5.99 ± 0.27 43.5 (41.9–45.0) 9944 38,189 661 (89) 1683 (12)
L1_Perissodactyla4_II 5896 17.2 ± 0.50 8.9 ± 0.27 66.2 (64.2–68.1) 9002 8807 94 (18) 127 (1)
L1_Perissodactyla5_I 5801 11.3 ± 0.40 6.4 ± 0.36 43.5 (41.9–45.0) 17,202 15,912 277 (33) 293 (2)
L1_Perissodactyla6_I 5828 16.40 ± 0.50 9.0 ± 0.39 63.1 (61.2–65.0) 13,988 13,692 274 (12) 308 (6)
L1_Perissodactyla7_I 6498 18.10 ± 0.60 10.7 ± 0.61 69.6 (67.3–71.9) 17,578 16,921 323 (11) 404 (10)
  1. Ec horse-specific, Cs rhinoceros-specific; perissodacyla = families that are shared between horse and rhinoceros. Family age was estimated using a substitution rate of 0.13%/myr. The number of full-length element was estimated by counting the number of 5’UTR generated by each family and the number estimated by GPS (in parenthesis)