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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_008554 | AP001637 | 124702729 | 1 | chr9 | NT_008554 | AC002101 | 124705378 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_008554 | AP001637 | 124702729 | 1 | chr9 | NT_008554 | AL357934 | 124911264 | 3 | 48744 | 3713 | 4156 | 56613 |
| S/G/Y/R/B/O |
NT_008554 | AP001637 | 124702729 | 1 | chr9 | NT_008554 | AL590710 | 124803352 | 3 | 58968 | 15630 | 4558 | 79156 |
| S/G/Y/R/B/O |
NT_008554 | AP001637 | 124702729 | 1 |   |   | AC000388 | 124629419 | 3 | 22517 | 8070 | 1325 | 31912 |
| S/G/Y/R/B/O |
NT_008554 | AP001637 | 124702729 | 1 |   |   | AC000402 | 124629419 | 3 | 15715 | 1660 | 1756 | 19131 |
| S/G/Y/R/B/O |
NT_008554 | AP001637 | 124702729 | 1 |   |   | AC002111 | 124629419 | 3 | 10902 | 2053 | 1341 | 14296 |
| S/G/Y/R/B/O |
NT_008554 | AP001637 | 124702729 | 1 |   |   | AC002295 | 124629419 | 3 | 24624 | 0 | 3108 | 27732 |
| S/G/Y/R/B/O |
NT_008554 | AP001637 | 124702729 | 1 |   |   | AC002297 | 124629419 | 3 | 14913 | 5804 | 2069 | 22786 |
| S/G/Y/R/B/O |
NT_008554 | AP001637 | 124702729 | 1 |   |   | AC002322 | 124629419 | 3 | 33535 | 0 | 0 | 33535 |
| S/G/Y/R/B/O |
NT_008554 | AP001637 | 124702729 | 1 |   |   | AL365494 | 124911264 | 1 | 39955 | 7814 | 1068 | 48837 |
| S/G/Y/R/B/O |
NT_008554 | AC002101 | 124705378 | 3 | chr9 | NT_008554 | AC001227 | 124749467 | 3 | 22147 | 0 | 0 | 22147 |
| S/G/Y/R/B/O |
NT_008554 | AC002101 | 124705378 | 3 |   |   | AC000033 | 124803352 | 3 | 35479 | 0 | 0 | 35479 |
| S/G/Y/R/B/O |
NT_008554 | AC001227 | 124749467 | 3 | chr9 | NT_008554 | AC000404 | 124764904 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_008554 | AC001227 | 124749467 | 3 |   |   | AL365494 | 124705378 | 1 | 15050 | 2055 | 0 | 17105 |
| S/G/Y/R/B/O |
NT_008554 | AC000404 | 124764904 | 3 | chr9 | NT_008554 | AL590710 | 124803352 | 3 | 10589 | 0 | 0 | 10589 |
| S/G/Y/R/B/O |
NT_008554 | AC000404 | 124764904 | 3 |   |   | AL365494 | 124705378 | 1 | 43416 | 0 | 0 | 43416 |
| S/G/Y/R/B/O |
NT_008554 | AL590710 | 124803352 | 3 | chr9 | NT_008554 | AL357934 | 124911264 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_008554 | AL590710 | 124803352 | 3 | chr9 | NT_008554 | AP001637 | 124702729 | 1 | 58968 | 15630 | 4558 | 79156 |
| S/G/Y/R/B/O |
NT_008554 | AL590710 | 124803352 | 3 |   |   | AC000388 | 124803352 | 3 | 48128 | 0 | 0 | 48128 |
| S/G/Y/R/B/O |
NT_008554 | AL590710 | 124803352 | 3 |   |   | AC002295 | 124764904 | 3 | 32364 | 0 | 0 | 32364 |
| S/G/Y/R/B/O |
NT_008554 | AL590710 | 124803352 | 3 |   |   | AC002297 | 124764904 | 3 | 36961 | 0 | 0 | 36961 |
| S/G/Y/R/B/O |
NT_008554 | AL590710 | 124803352 | 3 |   |   | AL365494 | 124764904 | 1 | 84718 | 4891 | 8270 | 97879 |
| S/G/Y/R/B/O |
NT_008554 | AL357934 | 124911264 | 3 | chr9 | NT_008554 | AL445931 | 125004769 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_008554 | AL357934 | 124911264 | 3 | chr9 | NT_008554 | AP001637 | 124702729 | 1 | 48744 | 3713 | 4156 | 56613 |
| S/G/Y/R/B/O |
NT_008554 | AL357934 | 124911264 | 3 |   |   | AC000402 | 124702729 | 3 | 27681 | 0 | 0 | 27681 |
| S/G/Y/R/B/O |
NT_008554 | AL357934 | 124911264 | 3 |   |   | AC002111 | 124702729 | 3 | 37403 | 0 | 0 | 37403 |
| S/G/Y/R/B/O |
NT_008554 | AL357934 | 124911264 | 3 |   |   | AC002322 | 124702729 | 3 | 38990 | 0 | 0 | 38990 |
| S/G/Y/R/B/O |
NT_008554 | AL357934 | 124911264 | 3 |   |   | AL365494 | 124702729 | 1 | 35479 | 0 | 0 | 35479 |
| S/G/Y/R/B/O |
NT_008554 | AL445931 | 125004769 | 3 | chr9 | NT_008554 | AL591386 | 125177797 | 3 | 2000 | 0 | 0 | 2000 |
| S/G/Y/R/B/O |
NT_008554 | AL445931 | 125004769 | 3 |   |   | AC000391 | 124702729 | 3 | 23981 | 0 | 0 | 23981 |
| S/G/Y/R/B/O |
NT_008554 | AL445931 | 125004769 | 3 |   |   | AC000401 | 124702729 | 3 | 45691 | 0 | 0 | 45691 |
| S/G/Y/R/B/O |
NT_008554 | AL445931 | 125004769 | 3 |   |   | AC000402 | 124702729 | 3 | 12434 | 0 | 0 | 12434 |
| S/G/Y/R/B/O |
NT_008554 | AL445931 | 125004769 | 3 |   |   | AC000405 | 124702729 | 3 | 37903 | 0 | 0 | 37903 |
| S/G/Y/R/B/O |
NT_008554 | AL445931 | 125004769 | 3 |   |   | AC002102 | 124702729 | 3 | 37405 | 0 | 0 | 37405 |
| S/G/Y/R/B/O |
NT_008554 | AL445931 | 125004769 | 3 |   |   | AC002103 | 124702729 | 3 | 38292 | 0 | 0 | 38292 |
| S/G/Y/R/B/O |
NT_008554 | AL445931 | 125004769 | 3 |   |   | AC002104 | 124702729 | 3 | 46615 | 0 | 0 | 46615 |
| S/G/Y/R/B/O |
NT_008554 | AL445931 | 125004769 | 3 |   |   | AC002293 | 124702729 | 3 | 18885 | 0 | 0 | 18885 |
| S/G/Y/R/B/O |
NT_008554 | AL445931 | 125004769 | 3 |   |   | Z81330 | 125177797 | 3 | 21573 | 0 | 0 | 21573 |
| S/G/Y/R/B/O |
NT_008554 | AL591386 | 125177797 | 3 |   |   |   |   |   |   |   |   |   |
| S/G/Y/R/B/O |
NT_008554 | AL591386 | 125177797 | 3 |   |   | AC000387 | 125177797 | 3 | 39118 | 0 | 0 | 39118 |
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