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Line color code:
- White: overlap with immediately succeeding clone
- Green: overlap with clone in same contig
- Pink: overlap with clone in same chromosome, different contig
- Red: overlap with clone on different chromosome
- Yellow: overlap with clone not used in assembly
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| Links | Contig1 | Acc1 | Start1 | Phs | Chr2 | Contig2 | Acc2 | Start2 | Phs | Strong Overlap | Medium Overlap | Weak Overlap | Total Overlap |
| S/G/Y/R/B/O |
NT_009609 | AC068297 | 52074878 | 1 | chr12 | NT_009609 | AC010188 | 52083711 | 3 | 81287 | 0 | 11297 | 92584 |
| S/G/Y/R/B/O |
NT_009609 | AC068297 | 52074878 | 1 | chr12 | NT_009609 | AC027750 | 52312966 | 1 | 43708 | 3758 | 0 | 47466 |
| S/G/Y/R/B/O |
NT_009609 | AC068297 | 52074878 | 1 | chr12 | NT_009609 | AC107031 | 52254441 | 1 | 38142 | 0 | 0 | 38142 |
| S/G/Y/R/B/O |
NT_009609 | AC068297 | 52074878 | 1 |   |   | AC046135 | 52312966 | 1 | 57370 | 5054 | 12263 | 74687 |
| S/G/Y/R/B/O |
NT_009609 | AC010188 | 52083711 | 3 | chr12 | NT_009609 | AC107031 | 52254441 | 1 | 38142 | 0 | 5334 | 43476 |
| S/G/Y/R/B/O |
NT_009609 | AC010188 | 52083711 | 3 | chr12 | NT_009609 | AC027750 | 52312966 | 1 | 43708 | 0 | 0 | 43708 |
| S/G/Y/R/B/O |
NT_009609 | AC010188 | 52083711 | 3 |   |   | AC046135 | 52312966 | 1 | 49479 | 2354 | 25933 | 77766 |
| S/G/Y/R/B/O |
NT_009609 | AC107031 | 52254441 | 1 | chr12 | NT_009609 | AC027750 | 52312966 | 1 | 132280 | 5919 | 14238 | 152437 |
| S/G/Y/R/B/O |
NT_009609 | AC107031 | 52254441 | 1 | chr12 | NT_009609 | AC025097 | 52343775 | 3 | 32857 | 0 | 0 | 32857 |
| S/G/Y/R/B/O |
NT_009609 | AC107031 | 52254441 | 1 | chr12 | NT_009609 | AC068297 | 52074878 | 1 | 38142 | 0 | 0 | 38142 |
| S/G/Y/R/B/O |
NT_009609 | AC107031 | 52254441 | 1 |   |   | AC046135 | 76385417 | 1 | 13303 | 0 | 0 | 13303 |
| S/G/Y/R/B/O |
NT_009609 | AC027750 | 52312966 | 1 | chr12 | NT_009609 | AC025097 | 52343775 | 3 | 25301 | 1625 | 0 | 26926 |
| S/G/Y/R/B/O |
NT_009609 | AC027750 | 52312966 | 1 | chr12 | NT_009609 | AC010188 | 52083711 | 3 | 43708 | 0 | 0 | 43708 |
| S/G/Y/R/B/O |
NT_009609 | AC027750 | 52312966 | 1 | chr12 | NT_009609 | AC068297 | 52074878 | 1 | 43708 | 3758 | 0 | 47466 |
| S/G/Y/R/B/O |
NT_009609 | AC027750 | 52312966 | 1 |   |   | AC046135 | 76385417 | 1 | 21256 | 1565 | 0 | 22821 |
| S/G/Y/R/B/O |
NT_009609 | AC025097 | 52343775 | 3 | chr12 | NT_009609 | AC027582 | 52525337 | 1 | 69895 | 1532 | 15665 | 87092 |
| S/G/Y/R/B/O |
NT_009609 | AC025097 | 52343775 | 3 | chr12 | NT_009609 | AC107031 | 52254441 | 1 | 32857 | 0 | 0 | 32857 |
| S/G/Y/R/B/O |
NT_009609 | AC025097 | 52343775 | 3 |   |   | AC023053 | 52254441 | 1 | 38512 | 2838 | 30998 | 72348 |
| S/G/Y/R/B/O |
NT_009609 | AC027582 | 52525337 | 1 | chr12 | NT_009609 | AC013758 | 52563767 | 1 | 27408 | 0 | 0 | 27408 |
| S/G/Y/R/B/O |
NT_009609 | AC027582 | 52525337 | 1 |   |   | AC023053 | 52563767 | 1 | 63672 | 8794 | 24848 | 97314 |
| S/G/Y/R/B/O |
NT_009609 | AC013758 | 52563767 | 1 | chr12 | NT_009609 | AC013421 | 52587547 | 1 | 103285 | 2253 | 7025 | 112563 |
| S/G/Y/R/B/O |
NT_009609 | AC013758 | 52563767 | 1 | chr12 | NT_009609 | AC027260 | 52625568 | 1 | 26496 | 3848 | 0 | 30344 |
| S/G/Y/R/B/O |
NT_009609 | AC013758 | 52563767 | 1 | chr12 | NT_009609 | AC068987 | 52646353 | 3 | 64359 | 3947 | 0 | 68306 |
| S/G/Y/R/B/O |
NT_009609 | AC013758 | 52563767 | 1 |   |   | AC023053 | 52587547 | 1 | 16280 | 1443 | 0 | 17723 |
| S/G/Y/R/B/O |
NT_009609 | AC013421 | 52587547 | 1 | chr12 | NT_009609 | AC027260 | 52625568 | 1 | 53874 | 2087 | 0 | 55961 |
| S/G/Y/R/B/O |
NT_009609 | AC013421 | 52587547 | 1 | chr12 | NT_009609 | AC025259 | 52729309 | 3 | 10249 | 0 | 0 | 10249 |
| S/G/Y/R/B/O |
NT_009609 | AC013421 | 52587547 | 1 | chr12 | NT_009609 | AC068987 | 52646353 | 3 | 49219 | 0 | 2447 | 51666 |
| S/G/Y/R/B/O |
NT_009609 | AC013421 | 52587547 | 1 |   |   | AC023053 | 52563767 | 1 | 11490 | 0 | 0 | 11490 |
| S/G/Y/R/B/O |
NT_009609 | AC027260 | 52625568 | 1 | chr12 | NT_009609 | AC068987 | 52646353 | 3 | 54176 | 2087 | 0 | 56263 |
| S/G/Y/R/B/O |
NT_009609 | AC027260 | 52625568 | 1 | chr12 | NT_009609 | AC013758 | 52563767 | 1 | 26496 | 3848 | 0 | 30344 |
| S/G/Y/R/B/O |
NT_009609 | AC027260 | 52625568 | 1 | chr12 | NT_009609 | AC019244 | 52929374 | 1 | 28465 | 0 | 0 | 28465 |
| S/G/Y/R/B/O |
NT_009609 | AC027260 | 52625568 | 1 | chr12 | NT_009609 | AC025259 | 52729309 | 3 | 69574 | 0 | 1495 | 71069 |
| S/G/Y/R/B/O |
NT_009609 | AC068987 | 52646353 | 3 | chr12 | NT_009609 | AC025259 | 52729309 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009609 | AC068987 | 52646353 | 3 | chr12 | NT_009609 | AC013421 | 52587547 | 1 | 49219 | 0 | 2447 | 51666 |
| S/G/Y/R/B/O |
NT_009609 | AC068987 | 52646353 | 3 | chr12 | NT_009609 | AC013758 | 52563767 | 1 | 64359 | 3947 | 0 | 68306 |
| S/G/Y/R/B/O |
NT_009609 | AC025259 | 52729309 | 3 | chr12 | NT_009609 | AC019244 | 52929374 | 1 | 131787 | 2050 | 0 | 133837 |
| S/G/Y/R/B/O |
NT_009609 | AC025259 | 52729309 | 3 | chr12 | NT_009609 | AC013421 | 52587547 | 1 | 10249 | 0 | 0 | 10249 |
| S/G/Y/R/B/O |
NT_009609 | AC025259 | 52729309 | 3 | chr12 | NT_009609 | AC027260 | 52625568 | 1 | 69574 | 0 | 1495 | 71069 |
| S/G/Y/R/B/O |
NT_009609 | AC025259 | 52729309 | 3 |   |   | AC080174 | 52961496 | 1 | 27340 | 0 | 0 | 27340 |
| S/G/Y/R/B/O |
NT_009609 | AC025259 | 52729309 | 3 |   |   | L31848 | 52961496 | 3 | 10849 | 0 | 0 | 10849 |
| S/G/Y/R/B/O |
NT_009609 | AC019244 | 52929374 | 1 | chr12 | NT_009609 | AC007101 | 52931085 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009609 | AC019244 | 52929374 | 1 | chr12 | NT_009609 | AC027260 | 52625568 | 1 | 28465 | 0 | 0 | 28465 |
| S/G/Y/R/B/O |
NT_009609 | AC019244 | 52929374 | 1 | chr12 | NT_009609 | AC078864 | 52961496 | 1 | 23420 | 2026 | 0 | 25446 |
| S/G/Y/R/B/O |
NT_009609 | AC007101 | 52931085 | 1 | chr12 | NT_009609 | AP002519 | 52931245 | 1 | 19714 | 3406 | 6016 | 29136 |
| S/G/Y/R/B/O |
NT_009609 | AC007101 | 52931085 | 1 | chr12 | NT_009609 | AC021066 | 53001748 | 3 | 16550 | 0 | 16947 | 33497 |
| S/G/Y/R/B/O |
NT_009609 | AC007101 | 52931085 | 1 |   |   | Y19215 | 52931245 | 3 | 10555 | 0 | 0 | 10555 |
| S/G/Y/R/B/O |
NT_009609 | AP002519 | 52931245 | 1 | chr12 | NT_009609 | AC078864 | 52961496 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009609 | AP002519 | 52931245 | 1 | chr12 | NT_009609 | AC021066 | 53001748 | 3 | 32452 | 0 | 1271 | 33723 |
| S/G/Y/R/B/O |
NT_009609 | AP002519 | 52931245 | 1 | chr12 | NT_009609 | AC027562 | 53602373 | 1 | 69295 | 0 | 1633 | 70928 |
| S/G/Y/R/B/O |
NT_009609 | AP002519 | 52931245 | 1 | chr12 | NT_009609 | AC078865 | 53507335 | 3 | 50905 | 0 | 1633 | 52538 |
| S/G/Y/R/B/O |
NT_009609 | AP002519 | 52931245 | 1 |   |   | Y19207 | 53507335 | 3 | 14674 | 0 | 0 | 14674 |
| S/G/Y/R/B/O |
NT_009609 | AP002519 | 52931245 | 1 |   |   | Y19213 | 53507335 | 3 | 11390 | 0 | 0 | 11390 |
| S/G/Y/R/B/O |
NT_009609 | AP002519 | 52931245 | 1 |   |   | Y19214 | 53507335 | 3 | 13599 | 1994 | 0 | 15593 |
| S/G/Y/R/B/O |
NT_009609 | AC078864 | 52961496 | 1 | chr12 | NT_009609 | AC021066 | 53001748 | 3 | 13242 | 0 | 10403 | 23645 |
| S/G/Y/R/B/O |
NT_009609 | AC078864 | 52961496 | 1 | chr12 | NT_009609 | AC019244 | 52929374 | 1 | 23420 | 2026 | 0 | 25446 |
| S/G/Y/R/B/O |
NT_009609 | AC078864 | 52961496 | 1 |   |   | AC080174 | 52729309 | 1 | 71721 | 0 | 16145 | 87866 |
| S/G/Y/R/B/O |
NT_009609 | AC021066 | 53001748 | 3 | chr12 | NT_009609 | AC068988 | 53150861 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009609 | AC021066 | 53001748 | 3 | chr12 | NT_009609 | AC007101 | 52931085 | 1 | 16550 | 0 | 16947 | 33497 |
| S/G/Y/R/B/O |
NT_009609 | AC021066 | 53001748 | 3 | chr12 | NT_009609 | AP002519 | 52931245 | 1 | 32452 | 0 | 1271 | 33723 |
| S/G/Y/R/B/O |
NT_009609 | AC021066 | 53001748 | 3 |   |   | AC080174 | 52961496 | 1 | 93850 | 4342 | 0 | 98192 |
| S/G/Y/R/B/O |
NT_009609 | AC068988 | 53150861 | 1 | chr12 | NT_009609 | AC055716 | 53161302 | 3 | 41048 | 5587 | 9016 | 55651 |
| S/G/Y/R/B/O |
NT_009609 | AC068988 | 53150861 | 1 | chr12 | NT_009609 | AC055715 | 53270086 | 3 | 28807 | 0 | 11487 | 40294 |
| S/G/Y/R/B/O |
NT_009609 | AC068988 | 53150861 | 1 |   |   | AC024196 | 52931245 | 1 | 12846 | 0 | 1484 | 14330 |
| S/G/Y/R/B/O |
NT_009609 | AC055716 | 53161302 | 3 | chr12 | NT_009609 | AC055715 | 53270086 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009609 | AC055716 | 53161302 | 3 |   |   | AC024196 | 53161302 | 1 | 43401 | 0 | 0 | 43401 |
| S/G/Y/R/B/O |
NT_009609 | AC055715 | 53270086 | 3 | chr12 | NT_009609 | AC055736 | 53356686 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009609 | AC055715 | 53270086 | 3 | chr12 | NT_009609 | AC068988 | 53150861 | 1 | 28807 | 0 | 11487 | 40294 |
| S/G/Y/R/B/O |
NT_009609 | AC055715 | 53270086 | 3 |   |   | AC024196 | 53150861 | 1 | 78791 | 0 | 1490 | 80281 |
| S/G/Y/R/B/O |
NT_009609 | AC055736 | 53356686 | 3 | chr12 | NT_009609 | AC078865 | 53507335 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009609 | AC055736 | 53356686 | 3 | chr12 | NT_009609 | AC027562 | 53602373 | 1 | 63068 | 1960 | 215 | 65243 |
| S/G/Y/R/B/O |
NT_009609 | AC055736 | 53356686 | 3 |   |   | AC024196 | 53150861 | 1 | 56352 | 0 | 0 | 56352 |
| S/G/Y/R/B/O |
NT_009609 | AC078865 | 53507335 | 3 | chr12 | NT_009609 | AC027562 | 53602373 | 1 | 61168 | 0 | 2763 | 63931 |
| S/G/Y/R/B/O |
NT_009609 | AC078865 | 53507335 | 3 | chr12 | NT_009609 | AP002519 | 52931245 | 1 | 50905 | 0 | 1633 | 52538 |
| S/G/Y/R/B/O |
NT_009609 | AC078865 | 53507335 | 3 |   |   | Y19207 | 52931245 | 3 | 14688 | 0 | 0 | 14688 |
| S/G/Y/R/B/O |
NT_009609 | AC078865 | 53507335 | 3 |   |   | Y19214 | 52931245 | 3 | 10643 | 0 | 0 | 10643 |
| S/G/Y/R/B/O |
NT_009609 | AC027562 | 53602373 | 1 |   |   |   |   |   |   |   |   |   |
| S/G/Y/R/B/O |
NT_009609 | AC027562 | 53602373 | 1 | chr12 | NT_009609 | AC055736 | 53356686 | 3 | 63068 | 1960 | 215 | 65243 |
| S/G/Y/R/B/O |
NT_009609 | AC027562 | 53602373 | 1 | chr12 | NT_009609 | AP002519 | 52931245 | 1 | 69295 | 0 | 1633 | 70928 |
| S/G/Y/R/B/O |
NT_009609 | AC027562 | 53602373 | 1 |   |   | Y19207 | 52931245 | 3 | 14682 | 0 | 0 | 14682 |
| S/G/Y/R/B/O |
NT_009609 | AC027562 | 53602373 | 1 |   |   | Y19213 | 52931245 | 3 | 11526 | 0 | 0 | 11526 |
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