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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_009368 | AC109309 | 1642495 | 2 | chr11 | NT_009368 | AC108448 | 1702860 | 2 | 8232 | 0 | 10104 | 18336 |
| S/G/Y/R/B/O |
NT_009368 | AC109309 | 1642495 | 2 | chr11 | NT_009368 | AC000378 | 1720501 | 3 | 10638 | 0 | 9950 | 20588 |
| S/G/Y/R/B/O |
NT_009368 | AC108448 | 1702860 | 2 | chr11 | NT_009368 | AC000378 | 1720501 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009368 | AC108448 | 1702860 | 2 | chr11 | NT_009368 | AC001228 | 2472311 | 3 | 26785 | 0 | 0 | 26785 |
| S/G/Y/R/B/O |
NT_009368 | AC108448 | 1702860 | 2 | chr11 | NT_009368 | AC016765 | 2705305 | 1 | 90515 | 3190 | 37563 | 131268 |
| S/G/Y/R/B/O |
NT_009368 | AC000378 | 1720501 | 3 | chr11 | NT_009368 | AC001236 | 1876365 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009368 | AC000378 | 1720501 | 3 | chr11 | NT_009368 | AC109309 | 1642495 | 2 | 10638 | 0 | 9950 | 20588 |
| S/G/Y/R/B/O |
NT_009368 | AC001236 | 1876365 | 1 | chr11 | NT_009368 | AC002536 | 1879802 | 3 | 88485 | 0 | 41140 | 129625 |
| S/G/Y/R/B/O |
NT_009368 | AC001236 | 1876365 | 1 | chr11 | NT_033238 | AC110059 | 1543105 | 2 | 19179 | 0 | 7910 | 27089 |
| S/G/Y/R/B/O |
NT_009368 | AC001236 | 1876365 | 1 |   |   | AC026645 | 1879802 | 1 | 23801 | 0 | 31867 | 55668 |
| S/G/Y/R/B/O |
NT_009368 | AC002536 | 1879802 | 3 | chr11 | NT_009368 | AC003693 | 2020779 | 3 | 2084 | 0 | 0 | 2084 |
| S/G/Y/R/B/O |
NT_009368 | AC002536 | 1879802 | 3 | chr11 | NT_033238 | AC110059 | 1543105 | 2 | 28386 | 0 | 0 | 28386 |
| S/G/Y/R/B/O |
NT_009368 | AC002536 | 1879802 | 3 |   |   | AC026645 | 2020779 | 1 | 46871 | 1730 | 42728 | 91329 |
| S/G/Y/R/B/O |
NT_009368 | AC003693 | 2020779 | 3 | chr11 | NT_009368 | AC000377 | 2173769 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009368 | AC003693 | 2020779 | 3 |   |   | AC000376 | 1543105 | 1 | 36067 | 0 | 13331 | 49398 |
| S/G/Y/R/B/O |
NT_009368 | AC003693 | 2020779 | 3 |   |   | AJ006343 | 1879802 | 3 | 33356 | 0 | 0 | 33356 |
| S/G/Y/R/B/O |
NT_009368 | AC003693 | 2020779 | 3 |   |   | AJ006345 | 1879802 | 3 | 95911 | 0 | 0 | 95911 |
| S/G/Y/R/B/O |
NT_009368 | AC000377 | 2173769 | 3 | chr11 | NT_009368 | AC002403 | 2236093 | 3 | 37334 | 0 | 0 | 37334 |
| S/G/Y/R/B/O |
NT_009368 | AC000377 | 2173769 | 3 |   |   | AJ006343 | 2236093 | 3 | 33462 | 0 | 0 | 33462 |
| S/G/Y/R/B/O |
NT_009368 | AC000377 | 2173769 | 3 |   |   | AJ006345 | 2236093 | 3 | 111214 | 0 | 0 | 111214 |
| S/G/Y/R/B/O |
NT_009368 | AC002403 | 2236093 | 3 | chr11 | NT_009368 | U90095 | 2331682 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009368 | AC002403 | 2236093 | 3 |   |   | AC021424 | 2173769 | 1 | 40651 | 3789 | 0 | 44440 |
| S/G/Y/R/B/O |
NT_009368 | AC002403 | 2236093 | 3 |   |   | AJ006345 | 2173769 | 3 | 132901 | 0 | 0 | 132901 |
| S/G/Y/R/B/O |
NT_009368 | U90095 | 2331682 | 3 | chr11 | NT_009368 | AC003675 | 2400281 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009368 | U90095 | 2331682 | 3 |   |   | AC021424 | 2173769 | 1 | 94776 | 14981 | 849 | 110606 |
| S/G/Y/R/B/O |
NT_009368 | U90095 | 2331682 | 3 |   |   | AJ006345 | 2173769 | 3 | 120189 | 0 | 0 | 120189 |
| S/G/Y/R/B/O |
NT_009368 | AC003675 | 2400281 | 3 | chr11 | NT_009368 | AC001228 | 2472311 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009368 | AC003675 | 2400281 | 3 | chr11 | NT_009368 | AC013791 | 2698428 | 1 | 28861 | 0 | 0 | 28861 |
| S/G/Y/R/B/O |
NT_009368 | AC003675 | 2400281 | 3 |   |   | AC021424 | 2698428 | 1 | 44657 | 7155 | 626 | 52438 |
| S/G/Y/R/B/O |
NT_009368 | AC003675 | 2400281 | 3 |   |   | AJ006345 | 2698428 | 3 | 86479 | 0 | 0 | 86479 |
| S/G/Y/R/B/O |
NT_009368 | AC001228 | 2472311 | 3 | chr11 | NT_009368 | AC013791 | 2698428 | 1 | 119165 | 0 | 0 | 119165 |
| S/G/Y/R/B/O |
NT_009368 | AC001228 | 2472311 | 3 | chr11 | NT_009368 | AC016765 | 2705305 | 1 | 36154 | 2964 | 0 | 39118 |
| S/G/Y/R/B/O |
NT_009368 | AC001228 | 2472311 | 3 | chr11 | NT_009368 | AC108448 | 1702860 | 2 | 26785 | 0 | 0 | 26785 |
| S/G/Y/R/B/O |
NT_009368 | AC001228 | 2472311 | 3 |   |   | AC005950 | 2698428 | 3 | 113314 | 0 | 0 | 113314 |
| S/G/Y/R/B/O |
NT_009368 | AC001228 | 2472311 | 3 |   |   | AJ006345 | 1702860 | 3 | 28607 | 0 | 0 | 28607 |
| S/G/Y/R/B/O |
NT_009368 | AC001228 | 2472311 | 3 |   |   | U51280 | 1702860 | 3 | 33219 | 0 | 0 | 33219 |
| S/G/Y/R/B/O |
NT_009368 | AC001228 | 2472311 | 3 |   |   | U51281 | 1702860 | 3 | 37908 | 0 | 0 | 37908 |
| S/G/Y/R/B/O |
NT_009368 | AC013791 | 2698428 | 1 | chr11 | NT_009368 | AC016765 | 2705305 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009368 | AC013791 | 2698428 | 1 | chr11 | NT_009368 | AC003675 | 2400281 | 3 | 28861 | 0 | 0 | 28861 |
| S/G/Y/R/B/O |
NT_009368 | AC013791 | 2698428 | 1 |   |   | AC005950 | 2400281 | 3 | 137109 | 0 | 0 | 137109 |
| S/G/Y/R/B/O |
NT_009368 | AC013791 | 2698428 | 1 |   |   | AC021424 | 80563623 | 1 | 40247 | 7577 | 1878 | 49702 |
| S/G/Y/R/B/O |
NT_009368 | AC013791 | 2698428 | 1 |   |   | AJ006345 | 80412868 | 3 | 28857 | 0 | 0 | 28857 |
| S/G/Y/R/B/O |
NT_009368 | AC016765 | 2705305 | 1 |   |   |   |   |   |   |   |   |   |
| S/G/Y/R/B/O |
NT_009368 | AC016765 | 2705305 | 1 | chr11 | NT_009368 | AC001228 | 2472311 | 3 | 36154 | 2964 | 0 | 39118 |
| S/G/Y/R/B/O |
NT_009368 | AC016765 | 2705305 | 1 | chr11 | NT_009368 | AC108448 | 1702860 | 2 | 90515 | 3190 | 37563 | 131268 |
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