Table 1 Transposable elements and other repeats identified in C. vicina
From: Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina
Family | Name | Copies | Total size | Average | Longest | |
|---|---|---|---|---|---|---|
Class I (retrotransposons) | LTR/Gypsy-CsRn1 | CsRn1_Cv1 | 1 | 4294 | 4294 | 4294 |
LTR/Gypsy-Osvaldo | Cv_Isis-like | 1 | 10995 | 10995 | 10995 | |
LTR/Pao | Pao_Cv1 | 1 | 6420 | 6420 | 6420 | |
Total LTR | 3 | 3 | 21709 | 7236 | 10995 | |
3.54% | ||||||
LINE/CR1 | CR1-1_CV | 3 | 2703 | 901 | 1461 | |
LINE/CR1 | CR1-2_CV | 2 | 309 | 155 | 309 | |
LINE/CR1 | CR1-3_CV | 1 | 188 | 188 | 188 | |
LINE/Jockey | Jockey_Cv1 | 1 | 553 | 553 | 553 | |
LINE/Jockey | Jockey_Cv2 | 1 | 180 | 180 | 180 | |
LINE/LOA | LOA-1_Cv | 1 | 536 | 536 | 536 | |
LINE/LOA | LOA-2_Cv | 1 | 1636 | 1636 | 1636 | |
LINE/LOA | LOA-3_Cv | 1 | 157 | 157 | 157 | |
LINE/LOA | LOA-4_Cv | 1 | 294 | 294 | 294 | |
LINE/LOA | LOA-5_Cv | 1 | 447 | 447 | 447 | |
LINE/LOA | LOA-6_Cv | 3 | 2414 | 805 | 1157 | |
LINE/LOA | LOA-7_Cv | 1 | 472 | 472 | 472 | |
LINE/LOA | LOA-8_Cv | 1 | 129 | 129 | 129 | |
LINE/LOA | LOA-9_Cv | 1 | 83 | 83 | 83 | |
LINE/LOA | LOA-10_Cv | 2 | 890 | 445 | 660 | |
LINE/L2 | L2-1_Cv | 1 | 315 | 315 | 315 | |
LINE/RTE | RTE-1_Cv | 1 | 1111 | 1111 | 1111 | |
LINE/RTE | RTE-2_Cv | 1 | 726 | 726 | 726 | |
LINE | LINE1_Cv | 1 | 276 | 276 | 276 | |
LINE | LINE2_Cv | 3 | 2541 | 847 | 2125 | |
LINE | LINE3_Cv | 1 | 2116 | 2116 | 2116 | |
Total LINE | 21 | 29 | 18076 | 623 | 2125 | |
2.95% | ||||||
Class II (DNA transposons) | DNA/ITm-mariner | Cv-mar1 | 40 | 30549 | 764 | 1296 |
DNA/ITm-mariner | Cv-mar2 | 14 | 6154 | 440 | 989 | |
DNA/ITm-mariner | Cv-mar3 | 5 | 950 | 190 | 311 | |
DNA/ITm-mariner | Cv-mar5 | 1 | 427 | 427 | 427 | |
DNA/ITm-DD37E | DD37E_Cv1 | 4 | 3073 | 768 | 1304 | |
DNA/ITm-Tc1 | AMARI_Cv1 | 5 | 1863 | 373 | 657 | |
DNA/ITm-Tc1 | SMAR_CV1 | 1 | 357 | 357 | 357 | |
DNA/ITm-Tc1 | CRMAR_CV1 | 1 | 305 | 305 | 305 | |
DNA/ITm-Tc3 | Tc3_CV1 | 1 | 356 | 356 | 356 | |
DNA/ITm-Tc3 | Tc3_CV2 | 1 | 414 | 414 | 414 | |
DNA/MITE | MITE_Cv1 | 8 | 1524 | 191 | 245 | |
DNA/Chapaev-Chapaev3 | Chapaev3-1_CV | 2 | 1658 | 829 | 1075 | |
DNA/Chapaev-Chapaev3 | Chapaev3-2_CV | 1 | 302 | 302 | 302 | |
DNA/hAT | hAT_CV1 | 2 | 265 | 133 | 163 | |
Total DNA | 14 | 86 | 48197 | 560 | 1304 | |
7.86% | ||||||
RC/Helitron | Helitron1-Cv | 3 | 1431 | 477 | 1269 | |
RC/Helitron | Helitron2-Cv | 41 | 19310 | 471 | 767 | |
RC/Helitron | Helitron3-Cv | 40 | 9901 | 248 | 821 | |
RC/Helitron | Helitron4-Cv | 1 | 85 | 85 | 85 | |
Total RC | 4 | 85 | 30727 | 361 | 1269 | |
5.01% | ||||||
Unclassified | Unknown | unknown1 | 4 | 2637 | 659 | 1010 |
Unknown | unknown2 | 5 | 542 | 108 | 127 | |
Unknown | unknown3 | 4 | 1459 | 365 | 521 | |
Unknown | unknown4 | 1 | 535 | 535 | 535 | |
Unknown | unknown5 | 20 | 4144 | 207 | 269 | |
Unknown | unknown6 | 12 | 3283 | 273 | 482 | |
Unknown | unknown7 | 4 | 3088 | 772 | 1009 | |
Unknown | unknown8 | 6 | 2051 | 342 | 600 | |
Unknown | unknown9 | 1 | 160 | 160 | 160 | |
Unknown | unknown10 | 5 | 598 | 120 | 130 | |
Unknown | unknown12 | 2 | 228 | 114 | 228 | |
Unknown | unknown13 | 7 | 3069 | 438 | 570 | |
Unknown | unknown14 | 2 | 246 | 123 | 129 | |
Unknown | unknown15 | 2 | 212 | 106 | 127 | |
Unknown | unknown16 | 1 | 151 | 151 | 151 | |
Unknown | unknown17 | 2 | 173 | 87 | 115 | |
Unknown | unknown18 | 3 | 658 | 219 | 247 | |
Unknown | unknown19 | 1 | 60 | 60 | 60 | |
Unknown | unknown20 | 10 | 1057 | 106 | 138 | |
Unknown | unknown21 | 1 | 55 | 55 | 55 | |
Unknown | unknown22 | 1 | 146 | 146 | 146 | |
Unknown | unknown23 | 8 | 3012 | 377 | 902 | |
Unknown | unknown24 | 1 | 138 | 138 | 138 | |
Unknown | unknown25 | 1 | 182 | 182 | 182 | |
Unknown | unknown26 | 1 | 242 | 242 | 242 | |
Unknown | unknown27 | 1 | 82 | 82 | 82 | |
Unknown | unknown28 | 1 | 137 | 137 | 137 | |
Unknown | unknown29 | 1 | 105 | 105 | 105 | |
Unknown | unknown30 | 1 | 108 | 108 | 108 | |
Unknown | unknown31 | 1 | 103 | 103 | 103 | |
Unknown | unknown32 | 1 | 110 | 110 | 110 | |
Unknown | unknown33 | 1 | 1429 | 1429 | 1429 | |
Unknown | unknown34 | 8 | 1913 | 239 | 359 | |
Total unknown | 33 | 120 | 32113 | 268 | 1429 | |
5.24% | ||||||
Total repeats | 75 | 323 | 150822 | |||
24.60% |