LTR Retrotransposons Characterized in This Study
| Element | Accession # | Genomic location | ITR | DTR | LTR length (bp) | Inserted element length | LTR % identity | Element age in millions of years |
| 17.6-1 | AC005860 | 2R/47D1 | AG/TT | ATAT/ATAT | 512 | 7202 | 100 | 0 |
| 17.6-2 | AC005894 | 2R/46A1-46B2 | AG/TT | ATAT/ATAT | 512 | 7200 | 100 | 0 |
| 17.6-3 | AC004333 | 3L/62A1-62A4 | AG/TT | ATAT/ATAT | 512 | 7245 | 100 | 0 |
| 17.6-4 | AE003471 | 3L | AG/TT | ATAT/ATAT | 514 | 6505 | 100 | 0 |
| 17.6-5 | AE003082 | 2R | AG/TT | ATAT/ATAT | 512 | 6329 | 99.419 | 0.181563 |
| 17.6-6 | AE003545 | 3L | AG/TT | ATAT/ATAT | 517 | 6509 | 99.189 | 0.253438 |
| 297-1 | AC006303 | 2L/35E-36A | AG/CT | ATAT/ATAT | 414 | 6808 | 100 | 0 |
| 297-2 | AC007176 | 2L-2R/37C1-46B2 | AG/CT | ATAT/ATAT | 414 | 6791 | 100 | 0 |
| 297-3 | AC005558 | 2L/23A1-23B2 | AG/CT | ATAT/ATAT | 414 | 6336 | 100 | 0 |
| 297-4 | AC005720 | 3L/79F1-80A2 | AG/CT | ATAT/ATAT | 414 | 6730 | 100 | 0 |
| 297-5 | AC004306 | 2R/51E1-51E2 | AG/CT | ATAT/ATAT | 414 | 6805 | 100 | 0 |
| 297-6 | AC002441 | 2L/35F3-35F6 | AG/CT | ATAT/ | 414/3′ LTR DELETION | 6809 | 100 | |
| 297-7 | AE003413 | 2L/34C4-36A7 | AG/CT | ATAT/ATAT | 414 | 6808 | 100 | 0 |
| 297-8 | AE003574 | X | AG/CT | ATAT/ATAT | 414 | 5708 | 100 | |
| 297-9 | AE003415 | SL/34C4-36A7 | AG/CT | ATAT/ATAT | 415 | 6809 | 100 | 0 |
| 297-10 | AE003599 | 3L | AG/CT | ATAT/ATAT | 414 | 5549 | 99.193 | 0.252188 |
| 412-1 | AC005847 | 3L/61F3-62A2 | TG/CT | ATAT/ACAG | 571 | 7592 | 99.789 | 0.065938 |
| 412-2 | AC005639 | 2R/59E3-59F4 | TG/CA | AGGG/AGGG | 481 | 7519 | 100 | 0 |
| 412-3 | AC005267 | 3L/60A2-60B2 | TG/CA | ATAT/ATAT | 514 | 7566 | 100 | 0 |
| 412-4 | AL050231 | X/1A-1B | TG/TA | CAAT/TATC | 512 | 7572 | 100 | 0 |
| 412-6 | AE003417 | X | TG/TA | CCAAT/TCGAC | 514 | 7578 | 99.415 | 0.182813 |
| 412-7 | AE003429 | X | TG/CA | TGAA/TGAA | 515 | 99.610 | 0.121875 | |
| 412-8 | AE003553 | 3L | TG/CA | GGGAGA/TGGCGA | 514 | 7582 | 99.805 | 0.060938 |
| 412-9 | AE003709 | 3R | TG/CA | CTAC/CTAC | 517 | 7558 | 99.368 | 0.197500 |
| 412-10 | AE003461 | 2R | TG/CA | AGGG/AGGG | 481 | 7452 | 100 | 0 |
| 412-11 | AE003462 | 2R | TG/CA | ATAT/ATAT | 518 | 7492 | 99.364 | 0.198750 |
| 412-12 | AE003463 | 2R | TG/CA | ATAG/ATAG | 482 | 7454 | 100 | 0 |
| 412-13 | AE003463 | 2R | TG/CA | CGAT/CGAT | 484 | 7461 | 99.583 | 0.130313 |
| 412-14 | AE003464 | 2R | TG/CA | AGTATG/CTAGAG | 472 | 7446 | 100 | 0 |
| 412-15 | AE003470 | 3L | TG/CA | GTCCTT/CAAGTC | 518 | 7529 | 100 | 0 |
| 412-16 | AE003470 | 3L | TG/CA | GATATA/ACAGCA | 572 | 7576 | 99.786 | 0.066875 |
| 412-17 | AE003511 | X | TG/CA | AAAC/AAAC | 514 | 7520 | 100 | 0 |
| 412-18 | AE003523 | 3L | TG/CA | GTGG/GTGG | 514 | 7520 | 99.790 | 0.065625 |
| 412-19 | AE003718 | 3R | TG/CA | ACAG/ACAG | 483 | 7550 | 100 | 0 |
| antonia-1 | AC005891 | 2L/33F3-34A2 | AG/TT | ATAT/ATAT | 659 | 6953 | 100 | 0 |
| antonia-2 | AC004362 | 2L/35E3-35E6 | AG/TT | ATAT/ATAT | 659 | 6943 | 100 | 0 |
| antonia-3 | AE003640 | 2L | AG/TT | ATAT/ATAT | 661 | 6170 | 99.697 | 0.094688 |
| antonia-4 | AE003786 | 2R | AG/TT | ATAT/ATAT | 661 | 6116 | 98.573 | 0.445938 |
| blastopia-1 | AC007177 | 2R/59C1-59C5 | TG/CA | TATA/TATA | 276 | 5029 | 100 | 0 |
| blastopia-2 | AC006402 | 2L/38C-38D | TG/CA | TATA/TATA | 276 | 5029 | 100 | 0 |
| blastopia-3 | AC005638 | 2R/47E1-47E3 | TG/CA | TTTA/TTTA | 276 | 4264 | 100 | 0 |
| blastopia-4 | AL033125 | DISTAL X | TG/CA | TATA/TATA | 276 | 4645 | 100 | 0 |
| blastopia-5 | AE003417 | X | TG/CA | TACA/TACA | 276 | 4272 | 100 | 0 |
| blastopia-6 | AE003489 | X | TG/CA | TGTA/TGTA | 275 | 3851 | 100 | 0 |
| blood-1 | AC002474 | 2L/38D1-38D2 | TG/CA | GTAC/GTAC | 399 | 7411 | 100 | 0 |
| blood-2 | AC005734 | 2L/31A1-31B1 | TG/CA | AAGG/AAGG | 401 | 7413 | 100 | 0 |
| blood-3 | AC004442 | 2L/22A3-22A7 | TG/CA | GTGG/GTGG | 399 | 7408 | 100 | 0 |
| blood-4 | AC005130 | 2L/39C1-39D1 | TG/CA | AGCA/AGCA | 399 | 7415 | 100 | 0 |
| blood-5 | AC007082 | 2L/37D | TG/CA | CCTG/CCTG | 401 | 7417 | 100 | 0 |
| blood-6 | L49394 | 2L/35E1-35E2 | TG/CA | AGGG/AGGG | 399 | 7411 | 100 | 0 |
| blood-7 | AC004115 | 2L/27B7-21C2 | TG/CA | GAAT/GAAT | 415 | 7443 | 99.758 | 0.07563 |
| blood-8 | AC003727 | 3R | TG/CA | ATAT/AGTC | 395 | 7425 | 99.500 | 0.15625 |
| blood-9 | AE003413 | 2L/34C4-36A7 | TG/CA | AGGG/AGGG | 399 | 7411 | 100 | 0 |
| blood-10 | AE003647 | 2L | TG/CA | AGGG/AGGG | 399 | 7421 | 100 | 0 |
| blood-11 | AE003718 | 3R | TG/CA | ATAC/ATAC | 399 | 7421 | 100 | 0 |
| blood-12 | AE003775 | 3R | TG/CA | GTAC/GTAC | 399 | 7421 | 100 | 0 |
| blood-13 | AE003555 | 3L | TG/CA | ACAT/ACAT | 400 | 7422 | 99.750 | 0.078125 |
| blood-14 | AE003667 | 2L | TG/CA | GTAC/GTAC | 400 | 7420 | 99.748 | 0.078750 |
| blood-15 | AE003670 | 2L | TG/CA | AGCA/AGCA | 400 | 7420 | 99.751 | 0.077813 |
| blood-16 | AE003633 | 2L | TG/CA | GCAG/GCAG | 400 | 7422 | 100 | 0 |
| blood-17 | AE003709 | 3R | TG/CA | ACAG/ACAG | 401 | 7425 | 100 | 0 |
| blood-18 | AE003598 | 3L | TG/CA | CTGC/CTGC | 401 | 7423 | 100 | 0 |
| blood-19 | AE003780 | 3R | TG/CA | CTAC/CTAC | 402 | 7427 | 100 | 0 |
| blood-20 | AE003589 | 2L | TG/CA | GAAT/GAAT | 415 | 7452 | 99.758 | 0.075625 |
| blood-21 | AE003638 | 2L | TG/CA | GTAC/GTAC | 377 | 7403 | 99.24 | 0.237500 |
| burdock-1 | AE002976 | 2R/41C-41D | AG/TT | TATA/TATA | 276 | 6425 | 100 | 0 |
| copia-1 | AC007146 | 2L/33A | TG/CA | GATCC/GATCC | 276 | 5146 | 100 | 0 |
| copia-2 | AC001657 | 2L/35B7-35C1 | TG/CA | GTTTC/GTTTC | 276 | 5145 | 100 | 0 |
| copia-3 | AC004445 | 2L/22A3-22A5 | TG/CA | GTTGG/GTTGG | 276 | 5145 | 100 | 0 |
| copia-4 | AC005554 | 2L/23C4-23D4 | TG/CA | TTATC/TTATC | 276 | 5145 | 100 | 0 |
| copia-5 | AC004276 | 2L/22E1-22E2 | TG/CA | GTATC/GTATC | 276 | 5147 | 100 | 0 |
| copia-6 | AC005647 | 2R/53C7-53C14 | TG/CA | TATGT/TATGT | 276 | 5151 | 100 | 0 |
| copia-7 | AC002501 | 2L/35F1-35F2 | TG/CA | AAAAT/AAAAT | 276 | 5149 | 100 | 0 |
| copia-8 | AC004735 | 2L/38A7-39C9 | TG/CA | GAGCA/GAGCA | 276 | 5144 | 100 | 0 |
| copia-9 | AC003053 | 2L/24A3-24C2 | TG/CA | ATCAC/ATCAC | 276 | 5145 | 100 | 0 |
| copia-10 | AC011662 | 2L/36D | TG/CA | ATAAC/ATAAC | 275 | 5145 | 100 | 0 |
| copia-11 | AC006215 | 2L/38C1-38C2 | TG/CA | ACTGC/ACTGC | 275 | 5252 | 100 | 0 |
| copia-12 | AE003494 | X | TG/CA | TTGAC/TTGAC | 276 | 4835 | 99.638 | 0.113125 |
| copia-14 | AE003794 | 2R | TG/CA | GGTTC/GGTTC | 276 | 4837 | 100 | 0 |
| copia-15 | AE003804 | 2R | TG/CA | ACGCC/ACGCC | 276 | 4742 | 100 | 0 |
| copia-16 | AE003777 | 3R | TG/CA | GATGG/GATGG | 277 | 4836 | 100 | 0 |
| copia-17 | AE003806 | 2R | TG/CA | TATGT/TATGT | 277 | 4511 | 99.628 | 0.116250 |
| copia-18 | AE003579 | 2L | TG/CA | ATCAC/ATCAC | 277 | 4747 | 100 | 0 |
| copia-19 | AE003729 | 3R | TG/CA | AAAAC/AAAAC | 277 | 4506 | 100 | 0 |
| copia-21 | AE003466 | 2R | TG/CA | CTTTG/CTCAG | 278 | 5176 | 100 | 0 |
| copia-22 | AE003783 | 2L | TG/CA | AACAC/AACAC | 278 | 4509 | 100 | 0 |
| copia-23 | AE003526 | 3L | TG/CA | AATAT/AATAT | 288 | 4564 | 100 | 0 |
| copia-24 | AE003778 | 3R | TG/CA | ATTAT/ATTAT | 307 | 4741 | 98.536 | 0.457500 |
| copia-25 | AE003473 | 3L | TG/CA | AGAAC/AGAAC | 276 | 4120 | 100 | 0 |
| hamilton-1 | AC006215 | 2L/38C1-38C2 | AG/TT | TGTA/TGTA | 495 | 6973 | 100 | 0 |
| hamilton-2 | AC006215 | 2L/38C1-38C2 | 495 | 6973 | 100 | 0 | ||
| HMS Beagle-1 | AC004563 | 2R/56D11-56E6 | AG/CT | TATA/TATA | 266 | 6883 | 100 | 0 |
| HMS Beagle-2 | AC007977 | 2L/27C | AG/CT | TATA/TATA | 266 | 6885 | 100 | 0 |
| HMS Beagle-3 | AL121804 | DISTAL X | AG/CT | TATA/TATT | 266 | 6887 | 100 | 0 |
| HMS Beagle-4 | AE003116 | 3L | AG/CT | TATA/TATA | 332 | 7180 | 99.034 | 0.301875 |
| HMS Beagle-5 | AE003574 | X | AG/CT | TGTA/TGTA | 332 | 7008 | 99.698 | 0.094375 |
| HMS Beagle-6 | AE003600 | 3R | AG/CT | TATA/TATA | 332 | 7217 | 100 | 0 |
| HMS Beagle-7 | AE003679 | AG/CT | TGCA/TGCA | 266 | 4441 | 100 | 0 | |
| HMS Beagle-8 | AE003651 | 2L | AG/CT | TGTA/TGTA | 266 | 6906 | 100 | 0 |
| mazi-1 | AC004377 | 2R/58E8-58F4 | TG/CA | ATGCTT/ATGGAA | 224 | 6112 | 100 | 0 |
| mazi-2 | AE003482 | 3L | TG/CA | AAGGG/AAGGG | 245 | 6150 | 100 | 0 |
| mazi-3 | AE003615 | 2L | TG/CA | GCTGG/GCTGG | 245 | 6148 | 100 | 0 |
| mazi-4 | AE003777 | 3R | TG/CA | AGTGT/AGTGT | 245 | 6149 | 100 | 0 |
| mdg1-1 | AL138971 | DISTAL X | TG/CA | CTAG/CTAG | 442 | 7355 | 100 | 0 |
| mdg1-2 | AE003736 | 3R | TG/CA | CTCC/CTCC | 442 | 8170 | 99.582 | 0.130625 |
| mdg1-3 | AE003828 | 2R | TG/CA | TCAC/TCAC | 444 | 7420 | 99.320 | 0.212500 |
| mdg1-4 | AE002943 | TG/CA | CTAT/CTAT | 425 | 8213 | 100 | 0 | |
| mdg3-1 | AC004574 | 2L/22B1-22B2 | TG/AA | GTAG/GTAG | 267 | 5519 | 100 | 0 |
| mdg3-2 | AC004735 | 2L/38A7-38C9 | TG/AA | GCAC/GCAC | 267 | 5504 | 100 | 0 |
| mdg3-3 | AE003607 | 3R | TG/AA | ATTG/ATTG | 265 | 5526 | 100 | 0 |
| mdg3-4 | AE003492 | X | TG/AA | ATGT/ATGT | 267 | 5399 | 100 | 0 |
| mdg3-5 | AE003514 | 3L | TG/AA | GTAT/GTAT | 267 | 5331 | 100 | 0 |
| mdg3-6 | AE003604 | 3R | TG/AA | CCAT/CCAT | 267 | 5330 | 100 | 0 |
| mdg3-7 | AE003686 | 3R | TG/AA | GTTG/GTTG | 267 | 5526 | 100 | 0 |
| mdg3-8 | AE003502 | X | TG/AA | TACT/TACT | 268 | 5529 | 99.247 | 0.235313 |
| micropia-1 | AE003672 | 3R | TG/CA | TATA/TATA | 514 | 5124 | 99.405 | 0.185938 |
| nik | AE003485 | X | AG/TT | CCAG/CCAG | 430 | 6938 | 100 | 0 |
| nomad-1 | AE003411 | 2L/35B4-35C1 | AG/CT | TTATA/TATA | 518 | 7389 | 100 | 0 |
| nomad-2 | AC004716 | 2L/22C1-22C2 | AG/CT | TTTA/TTTA | 518 | 7473 | 100 | 0 |
| nomad-3 | AC005111 | 2L/31F5-32A1 | AG/CT | TTCA/TTCA | 518 | 7473 | 100 | 0 |
| nomad-4 | AL121805 | DISTAL X | AG/CT | TATA/TATA | 517 | 7475 | 100 | 0 |
| roo-1 | AC005333 | 2L/26A1-26A3 | TG/CA | GGTAC/GGTAC | 428 | 8067 | 100 | 0 |
| roo-2 | AC004728 | 2L/29D1 | TG/CA | AGCGC/AGCGC | 429 | 8218 | 100 | 0 |
| roo-3 | AC001647 | 2R/35A1 | TG/CA | GTTAT/GTTAT | 428 | 8211 | 100 | 0 |
| roo-4 | AC001659 | 2L/34D1-34D4 | TG/CA | CTAAC/CTAAC | 429 | 8209 | 99.528 | 0.147500 |
| roo-5 | AC007453 | 2R/49D1-49D3 | TG/CA | TGGCC/TGGCC | 428 | 7411 | 100 | 0 |
| roo-6 | AC004438 | 3L/68C2-68C3 | TG/CA | CATTT/CATTT | 428 | 8251 | 99.766 | 0.073125 |
| roo-7 | AC004767 | 3L/65A6-65A10 | TG/CA | AACGG/AACGG | 428 | 8211 | 99.766 | 0.073125 |
| roo-8 | AC004245 | 2L/21D1-21D2 | TG/CA | GCCCC/GCCCC | 428 | 8087 | 100 | 0 |
| roo-9 | AC005974 | 2R/46E1-46F6 | TG/CA | TGTAT/TGTAT | 428 | 8215 | 99.766 | 0.073125 |
| roo-10 | AC011662 | 2L/36D | TG/CA | CCCCC/CCCCC | 428 | 8209 | 100 | 0 |
| roo-11 | AC006415 | 2L/40B-40C | TG/CA | GCTTCC/GCTTCC | 428 | 8212 | 100 | 0 |
| roo-12 | AL035311 | DISTAL TIP OF X | TG/CA | GCATC/GCATC | 427 | 7788 | 100 | 0 |
| roo-13 | AL121805 | DISTAL TIP OF X | TG/CA | TTAAT/TTAAT | 428 | 8197 | 100 | 0 |
| roo-14 | AC004349 | 3L/65B1-65B2 | TG/CA | TAATA/ | 428/3′ END DELETION | 5895 | 100 | 0 |
| roo-16 | AL031366 | DISTAL TIP OF X | TG/CA | ATTA/ATTA | 428 | 7758 | 100 | 0 |
| roo-17 | AL138971 | DISTAL X | TG/CA | GGGAC/GGGAC | 428 | 7593 | 100 | 0 |
| roo-19 | AE003606 | 3R | TG/CA | ATAAG/ATAAG | 429 | 8211 | 100 | 0 |
| roo-21 | AE003428 | X | TG/CA | CATAC/CCAGA | 429 | 8086 | 99.532 | 0.146250 |
| roo-22 | AE003703 | 3R | TG/CA | AGAC/AGAC | 429 | 8317 | 99.766 | 0.073125 |
| roo-23 | AE003497 | X | TG/CA | GTCAT/GTCAT | 429 | 8087 | 100 | 0 |
| roo-24 | AE003552 | 3L | TG/CA | TGGAG/TGGAG | 429 | 8086 | 100 | 0 |
| roo-25 | AE003421 | X | TG/CA | CAGCT/CAGCT | 430 | 8251 | 100 | 0 |
| roo-26 | AE003773 | 3R | TG/CA | CAAAT/CAAAT | 430 | 7332 | 99.767 | 0.072813 |
| roo-27 | AE003753 | 3R | TG/CA | AGGGC/AGGGC | 430 | 8229 | 99.765 | 0.073438 |
| roo-28 | AE003756 | 3R | TG/CA | ATAGT/ATAGT | 430 | 8229 | 99.766 | 0.073125 |
| roo-29 | AE003455 | 2R | TG/CA | ACTAC/ACTAC | 431 | 8089 | 99.523 | 0.149063 |
| roo-30 | AE003544 | 3L | TG/CA | CATTT/CATTT | 431 | 8086 | 99.769 | 0.072188 |
| roo-31 | AE003679 | 3R | TG/CA | GCCGG/GCCGG | 431 | 8240 | 99.768 | 0.072500 |
| roo-32 | AE003738 | 3R | TG/CA | AGACC/AGACC | 431 | 8240 | 99.766 | 0.073125 |
| roo-33 | AE003529 | 3L | TG/CA | ATAGG/ATAGG | 431 | 8087 | 100 | 0 |
| roo-34 | AE003470 | 3L | TG/CA | ATAA/ATAA | 432 | 8144 | 99.295 | 0.220313 |
| roo-35 | AE003455 | 2R | TG/CA | GCCAG/GCCAG | 432 | 8086 | 99.766 | 0.073125 |
| roo-36 | AE003519 | 2R | TG/CA | GAAGG/GAAGG | 432 | 8090 | 99.768 | 0.072500 |
| roo-37 | AE003520 | 3L | TG/CA | AATAG/AATAG | 432 | 8089 | 99.766 | 0.073125 |
| roo-38 | AE003467 | 3L | TG/CA | TAAAC/TAAAC | 433 | 8241 | 99.769 | 0.072188 |
| roo-39 | AE003515 | 3L | TG/CA | CTTGC/CTTGC | 433 | 8091 | 99.761 | 0.074688 |
| roo-40 | AE003419 | X | TG/CA | TTAC/TTAC | 434 | 8090 | 99.529 | 0.147188 |
| roo-41 | AE003781 | 2L | TG/CA | ATAAC/ATAAC | 431 | 8251 | 100 | 0 |
| roo-42 | AE003463 | 2R | TG/CA | CTTTA/CTTTA | 430 | 8088 | 100 | 0 |
| roo-43 | AE003410 | 2L, REGION 34C4-36A7 | TG/CA | ATAAC/ATAAC | 428 | 8142 | 100 | 0 |
| tirant-1 | AC005444 | 2L/36D3 | AG/CT | CGCG/CGCG | 417 | 8109 | 100 | 0 |
| tirant-2 | AC004759 | 2L/38E1-38E9 | AG/CT | CCCG/CCCG | 417 | 7399 | 100 | 0 |
| tirant-3 | AE003829 | 2R | AG/CT | CGTG/CGTG | 418 | 8016 | 100 | 0 |
| tirant-4 | AE003601 | 3R | AG/CT | CCCG/CCCG | 418 | 8016 | 100 | 0 |
| tirant-5 | AE003593 | 3L | AG/CT | CGCG/CGCG | 418 | 8016 | 100 | 0 |
| tirant-6 | AE003843 | 4 | AG/CT | CGCT/CGAT | 419 | 8017 | 100 | 0 |
| transpac-1 | AC006302 | 2L/34C4-34D2 | AG/CT | ATAT/ATAT | 330 | 5249 | 100 | 0 |
| transpac-2 | AE003426 | X | AG/CT | ATAT/ATAT | 330 | 5251 | 100 | 0 |
| transpac-3 | AE003762 | 3R | AG/CT | ATAT/ATAT | 330 | 5247 | 100 | 0 |
| transpac-4 | AE003508 | X | AG/CT | ATAT/ATAT | 331 | 5253 | 100 | 0 |
| wolfman-1 | AC007146 | 2L/33A-33A | TG/CA | AAGC/AAGC | 506 | 7345 | 100 | 0 |
| wolfman-2 | AE003439 | X | TG/CA | CCTG/CCTG | 506 | 7231 | 100 | 0 |
| unclassified | AE002665 | 3L | TG/CA | AATG/AATG | 266 | 7436 | 100 | 0 |
| unclassified | AE002987 | X | AG/TT | TATA/TATA | 414 | 8437 | 99.510 | 0.153125 |
| unclassified | AE003268 | AG/CT | TATA/TATA | 416 | 7185 | 99.760 | 0.075120 | |
| unclassified | AE003450 | X | AG/TT | TATA/TATA | 405 | 6538 | 100 | 0 |
| unclassified | AL035631 | DISTAL X | AG/TT | TCTA/TCTA | 353 | 5023 | 99.433 | 0.177054 |