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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_030874 | AC096508 | 5714904 | 1 | chrX | NT_030874 | AC068676 | 5715108 | 1 | 65100 | 1632 | 0 | 66732 |
| S/G/Y/R/B/O |
NT_030874 | AC096508 | 5714904 | 1 | chrX | NT_030874 | AC002549 | 6003355 | 3 | 52037 | 0 | 0 | 52037 |
| S/G/Y/R/B/O |
NT_030874 | AC096508 | 5714904 | 1 | chrX | NT_030874 | AC073488 | 5716414 | 1 | 38299 | 0 | 33521 | 71820 |
| S/G/Y/R/B/O |
NT_030874 | AC068676 | 5715108 | 1 | chrX | NT_030874 | AC073488 | 5716414 | 1 | 49454 | 0 | 0 | 49454 |
| S/G/Y/R/B/O |
NT_030874 | AC068676 | 5715108 | 1 | chrX | NT_030874 | AC002549 | 6003355 | 3 | 133645 | 1626 | 16369 | 151640 |
| S/G/Y/R/B/O |
NT_030874 | AC073488 | 5716414 | 1 | chrX | NT_030874 | AC003684 | 5776336 | 3 | 42645 | 0 | 0 | 42645 |
| S/G/Y/R/B/O |
NT_030874 | AC073488 | 5716414 | 1 | chrX | NT_030874 | AC002549 | 6003355 | 3 | 10758 | 0 | 0 | 10758 |
| S/G/Y/R/B/O |
NT_030874 | AC073488 | 5716414 | 1 | chrX | NT_030874 | AC096508 | 5714904 | 1 | 38299 | 0 | 33521 | 71820 |
| S/G/Y/R/B/O |
NT_030874 | AC003684 | 5776336 | 3 | chrX | NT_030874 | AC002549 | 6003355 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_030874 | AC002549 | 6003355 | 3 | chrX | NT_030874 | AC003036 | 6166382 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_030874 | AC002549 | 6003355 | 3 | chrX | NT_030874 | AC068676 | 5715108 | 1 | 133645 | 1626 | 16369 | 151640 |
| S/G/Y/R/B/O |
NT_030874 | AC002549 | 6003355 | 3 | chrX | NT_030874 | AC073488 | 5716414 | 1 | 10758 | 0 | 0 | 10758 |
| S/G/Y/R/B/O |
NT_030874 | AC002549 | 6003355 | 3 | chrX | NT_030874 | AC096508 | 5714904 | 1 | 52037 | 0 | 0 | 52037 |
| S/G/Y/R/B/O |
NT_030874 | AC003036 | 6166382 | 3 | chrX | NT_030874 | AC090481 | 6289414 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_030874 | AC003036 | 6166382 | 3 | chrX | NT_030874 | AC022082 | 6331910 | 1 | 37422 | 0 | 54564 | 91986 |
| S/G/Y/R/B/O |
NT_030874 | AC003036 | 6166382 | 3 |   |   | AC024217 | 6331910 | 1 | 96444 | 0 | 0 | 96444 |
| S/G/Y/R/B/O |
NT_030874 | AC090481 | 6289414 | 3 | chrX | NT_030874 | AC022082 | 6331910 | 1 | 24560 | 2667 | 4054 | 31281 |
| S/G/Y/R/B/O |
NT_030874 | AC090481 | 6289414 | 3 |   |   | AC003047 | 6331910 | 3 | 39108 | 0 | 0 | 39108 |
| S/G/Y/R/B/O |
NT_030874 | AC022082 | 6331910 | 1 |   |   |   |   |   |   |   |   |   |
| S/G/Y/R/B/O |
NT_030874 | AC022082 | 6331910 | 1 | chrX | NT_030874 | AC003036 | 6166382 | 3 | 37422 | 0 | 54564 | 91986 |
| S/G/Y/R/B/O |
NT_030874 | AC022082 | 6331910 | 1 | chr9 | NT_008476 | AL354991 | 83438662 | 3 | 23678 | 0 | 0 | 23678 |
| S/G/Y/R/B/O |
NT_030874 | AC022082 | 6331910 | 1 | chr9 | NT_008476 | AL583839 | 83473606 | 3 | 39721 | 0 | 22159 | 61880 |
| S/G/Y/R/B/O |
NT_030874 | AC022082 | 6331910 | 1 |   |   | AC003047 | 6166382 | 3 | 24376 | 4680 | 2015 | 31071 |
| S/G/Y/R/B/O |
NT_030874 | AC022082 | 6331910 | 1 |   |   | AC024217 | 6166382 | 1 | 42933 | 0 | 33374 | 76307 |
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