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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_028310 | AC060812 | 2905761 | 1 | chr11 | NT_028310 | AC090587 | 2991617 | 1 | 41180 | 0 | 42381 | 83561 |
| S/G/Y/R/B/O |
NT_028310 | AC060812 | 2905761 | 1 | chr11 | NT_028310 | AC018803 | 3034626 | 1 | 29226 | 5439 | 6405 | 41070 |
| S/G/Y/R/B/O |
NT_028310 | AC060812 | 2905761 | 1 |   |   | AF327367 | 2991617 | 3 | 12285 | 0 | 0 | 12285 |
| S/G/Y/R/B/O |
NT_028310 | AC090587 | 2991617 | 1 | chr11 | NT_028310 | AC018803 | 3034626 | 1 | 62050 | 7289 | 17405 | 86744 |
| S/G/Y/R/B/O |
NT_028310 | AC090587 | 2991617 | 1 | chr11 | NT_028310 | AC090804 | 3098222 | 1 | 32414 | 0 | 893 | 33307 |
| S/G/Y/R/B/O |
NT_028310 | AC018803 | 3034626 | 1 | chr11 | NT_028310 | AC090804 | 3098222 | 1 | 28982 | 2634 | 0 | 31616 |
| S/G/Y/R/B/O |
NT_028310 | AC018803 | 3034626 | 1 | chr11 | NT_028310 | AC060812 | 2905761 | 1 | 29226 | 5439 | 6405 | 41070 |
| S/G/Y/R/B/O |
NT_028310 | AC090804 | 3098222 | 1 | chr11 | NT_028310 | AC018888 | 3154608 | 1 | 51018 | 8629 | 0 | 59647 |
| S/G/Y/R/B/O |
NT_028310 | AC090804 | 3098222 | 1 | chr11 | NT_028310 | AC087441 | 3168118 | 1 | 92507 | 0 | 1335 | 93842 |
| S/G/Y/R/B/O |
NT_028310 | AC090804 | 3098222 | 1 | chr11 | NT_028310 | AC090587 | 2991617 | 1 | 32414 | 0 | 893 | 33307 |
| S/G/Y/R/B/O |
NT_028310 | AC090804 | 3098222 | 1 | chr11 | NT_028310 | AC107970 | 3309445 | 3 | 65819 | 0 | 1344 | 67163 |
| S/G/Y/R/B/O |
NT_028310 | AC018888 | 3154608 | 1 | chr11 | NT_028310 | AC087441 | 3168118 | 1 | 111314 | 14240 | 6083 | 131637 |
| S/G/Y/R/B/O |
NT_028310 | AC018888 | 3154608 | 1 | chr11 | NT_028310 | AC107970 | 3309445 | 3 | 84085 | 14235 | 3488 | 101808 |
| S/G/Y/R/B/O |
NT_028310 | AC018888 | 3154608 | 1 |   |   | AC090831 | 3098222 | 1 | 48102 | 7128 | 3488 | 58718 |
| S/G/Y/R/B/O |
NT_028310 | AC087441 | 3168118 | 1 | chr11 | NT_028310 | AC107970 | 3309445 | 3 | 124392 | 0 | 0 | 124392 |
| S/G/Y/R/B/O |
NT_028310 | AC087441 | 3168118 | 1 | chr11 | NT_028310 | AC090804 | 3098222 | 1 | 92507 | 0 | 1335 | 93842 |
| S/G/Y/R/B/O |
NT_028310 | AC087441 | 3168118 | 1 |   |   | AC090831 | 3098222 | 1 | 71419 | 0 | 0 | 71419 |
| S/G/Y/R/B/O |
NT_028310 | AC107970 | 3309445 | 3 | chr11 | NT_028310 | AC015689 | 3339779 | 1 | 23452 | 0 | 0 | 23452 |
| S/G/Y/R/B/O |
NT_028310 | AC107970 | 3309445 | 3 | chr11 | NT_028310 | AC018888 | 3154608 | 1 | 84085 | 14235 | 3488 | 101808 |
| S/G/Y/R/B/O |
NT_028310 | AC107970 | 3309445 | 3 | chr11 | NT_028310 | AC090804 | 3098222 | 1 | 65819 | 0 | 1344 | 67163 |
| S/G/Y/R/B/O |
NT_028310 | AC107970 | 3309445 | 3 |   |   | AC090831 | 3098222 | 1 | 79733 | 0 | 0 | 79733 |
| S/G/Y/R/B/O |
NT_028310 | AC015689 | 3339779 | 1 | chr11 | NT_028310 | AC016035 | 3507354 | 1 | 0 | 1648 | 0 | 1648 |
| S/G/Y/R/B/O |
NT_028310 | AC015689 | 3339779 | 1 |   |   | AC090831 | 3507354 | 1 | 32843 | 0 | 0 | 32843 |
| S/G/Y/R/B/O |
NT_028310 | AC015689 | 3339779 | 1 |   |   | AF391285 | 3309445 | 3 | 145714 | 1648 | 0 | 147362 |
| S/G/Y/R/B/O |
NT_028310 | AC016035 | 3507354 | 1 | chr11 | NT_028310 | AC018793 | 3528975 | 1 | 47024 | 0 | 89055 | 136079 |
| S/G/Y/R/B/O |
NT_028310 | AC016035 | 3507354 | 1 |   |   | AF391284 | 3528975 | 3 | 10398 | 0 | 0 | 10398 |
| S/G/Y/R/B/O |
NT_028310 | AC016035 | 3507354 | 1 |   |   | AF391285 | 3528975 | 3 | 27703 | 0 | 0 | 27703 |
| S/G/Y/R/B/O |
NT_028310 | AC018793 | 3528975 | 1 | chr11 | NT_028310 | AC009758 | 3640499 | 3 | 58368 | 0 | 0 | 58368 |
| S/G/Y/R/B/O |
NT_028310 | AC018793 | 3528975 | 1 |   |   | AF101874 | 3507354 | 3 | 10693 | 0 | 0 | 10693 |
| S/G/Y/R/B/O |
NT_028310 | AC018793 | 3528975 | 1 |   |   | AF391283 | 3507354 | 3 | 56934 | 0 | 0 | 56934 |
| S/G/Y/R/B/O |
NT_028310 | AC018793 | 3528975 | 1 |   |   | AF391284 | 3507354 | 3 | 19805 | 0 | 0 | 19805 |
| S/G/Y/R/B/O |
NT_028310 | AC018793 | 3528975 | 1 |   |   | U01882 | 3507354 | 3 | 13222 | 0 | 0 | 13222 |
| S/G/Y/R/B/O |
NT_028310 | AC009758 | 3640499 | 3 | chr11 | NT_028310 | AC010930 | 3781984 | 3 | 65261 | 0 | 0 | 65261 |
| S/G/Y/R/B/O |
NT_028310 | AC009758 | 3640499 | 3 |   |   | AC079759 | 3528975 | 1 | 31820 | 11422 | 26103 | 69345 |
| S/G/Y/R/B/O |
NT_028310 | AC009758 | 3640499 | 3 |   |   | AF101874 | 3528975 | 3 | 10701 | 0 | 0 | 10701 |
| S/G/Y/R/B/O |
NT_028310 | AC009758 | 3640499 | 3 |   |   | AF391283 | 3528975 | 3 | 82716 | 0 | 0 | 82716 |
| S/G/Y/R/B/O |
NT_028310 | AC009758 | 3640499 | 3 |   |   | U01882 | 3528975 | 3 | 13223 | 0 | 0 | 13223 |
| S/G/Y/R/B/O |
NT_028310 | AC010930 | 3781984 | 3 | chr11 | NT_028310 | AC090719 | 3864927 | 2 | 58290 | 0 | 0 | 58290 |
| S/G/Y/R/B/O |
NT_028310 | AC010930 | 3781984 | 3 |   |   | AC025249 | 3640499 | 1 | 13425 | 0 | 0 | 13425 |
| S/G/Y/R/B/O |
NT_028310 | AC010930 | 3781984 | 3 |   |   | AC027367 | 3640499 | 1 | 33458 | 1508 | 1548 | 36514 |
| S/G/Y/R/B/O |
NT_028310 | AC010930 | 3781984 | 3 |   |   | AC079759 | 3640499 | 1 | 39569 | 15697 | 47733 | 102999 |
| S/G/Y/R/B/O |
NT_028310 | AC010930 | 3781984 | 3 |   |   | AC105936 | 3864927 | 1 | 65403 | 0 | 0 | 65403 |
| S/G/Y/R/B/O |
NT_028310 | AC090719 | 3864927 | 2 | chr11 | NT_028310 | AC103710 | 3985813 | 3 | 12153 | 0 | 0 | 12153 |
| S/G/Y/R/B/O |
NT_028310 | AC090719 | 3864927 | 2 |   |   | AC025249 | 3781984 | 1 | 178921 | 0 | 0 | 178921 |
| S/G/Y/R/B/O |
NT_028310 | AC090719 | 3864927 | 2 |   |   | AC027367 | 3781984 | 1 | 118871 | 7408 | 26711 | 152990 |
| S/G/Y/R/B/O |
NT_028310 | AC090719 | 3864927 | 2 |   |   | AC105936 | 3985813 | 1 | 103686 | 0 | 0 | 103686 |
| S/G/Y/R/B/O |
NT_028310 | AC103710 | 3985813 | 3 | chr11 | NT_028310 | AC011711 | 4045307 | 3 | 80090 | 0 | 0 | 80090 |
| S/G/Y/R/B/O |
NT_028310 | AC103710 | 3985813 | 3 |   |   | AC025249 | 4045307 | 1 | 12146 | 0 | 0 | 12146 |
| S/G/Y/R/B/O |
NT_028310 | AC011711 | 4045307 | 3 | chr11 | NT_028310 | AC018375 | 4194849 | 3 | 31184 | 0 | 0 | 31184 |
| S/G/Y/R/B/O |
NT_028310 | AC018375 | 4194849 | 3 | chr11 | NT_028310 | AC090893 | 4313572 | 3 | 114161 | 0 | 0 | 114161 |
| S/G/Y/R/B/O |
NT_028310 | AC018375 | 4194849 | 3 | chr11 | NT_028310 | AC020597 | 4435256 | 1 | 101277 | 1599 | 3149 | 106025 |
| S/G/Y/R/B/O |
NT_028310 | AC018375 | 4194849 | 3 | chr11 | NT_033239 | AC113331 | 4486781 | 2 | 20709 | 0 | 0 | 20709 |
| S/G/Y/R/B/O |
NT_028310 | AC018375 | 4194849 | 3 |   |   | AL590419 | 4486781 | 2 | 48315 | 0 | 0 | 48315 |
| S/G/Y/R/B/O |
NT_028310 | AC090893 | 4313572 | 3 | chr11 | NT_028310 | U73627 | 4401290 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_028310 | AC090893 | 4313572 | 3 | chr11 | NT_028310 | AC020597 | 4435256 | 1 | 150083 | 6553 | 25362 | 181998 |
| S/G/Y/R/B/O |
NT_028310 | AC090893 | 4313572 | 3 | chr11 | NT_033239 | AC113331 | 4486781 | 2 | 20709 | 0 | 0 | 20709 |
| S/G/Y/R/B/O |
NT_028310 | AC090893 | 4313572 | 3 |   |   | AL590419 | 4486781 | 2 | 125382 | 0 | 0 | 125382 |
| S/G/Y/R/B/O |
NT_028310 | U73627 | 4401290 | 3 | chr11 | NT_028310 | AC020597 | 4435256 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_028310 | AC020597 | 4435256 | 1 |   |   |   |   |   |   |   |   |   |
| S/G/Y/R/B/O |
NT_028310 | AC020597 | 4435256 | 1 | chr11 | NT_028310 | AC018375 | 4194849 | 3 | 101277 | 1599 | 3149 | 106025 |
| S/G/Y/R/B/O |
NT_028310 | AC020597 | 4435256 | 1 | chr11 | NT_028310 | AC090893 | 4313572 | 3 | 150083 | 6553 | 25362 | 181998 |
| S/G/Y/R/B/O |
NT_028310 | AC020597 | 4435256 | 1 | chr11 | NT_033239 | AC113331 | 4486781 | 2 | 62700 | 4950 | 22083 | 89733 |
| S/G/Y/R/B/O |
NT_028310 | AC020597 | 4435256 | 1 |   |   | AL590419 | 4486781 | 2 | 81592 | 4952 | 22078 | 108622 |
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