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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_011657 | AL627091 | 34065570 | 3 | chrX | NT_011657 | AL356858 | 34095267 | 3 | 2000 | 0 | 0 | 2000 |
| S/G/Y/R/B/O |
NT_011657 | AL356858 | 34095267 | 3 | chrX | NT_011657 | AJ239329 | 34222235 | 3 | 0 | 0 | 100 | 100 |
| S/G/Y/R/B/O |
NT_011657 | AJ239329 | 34222235 | 3 | chrX | NT_011657 | AL627244 | 34328739 | 3 | 71763 | 0 | 0 | 71763 |
| S/G/Y/R/B/O |
NT_011657 | AL627244 | 34328739 | 3 | chrX | NT_011657 | AL121577 | 34407923 | 3 | 41868 | 0 | 0 | 41868 |
| S/G/Y/R/B/O |
NT_011657 | AL121577 | 34407923 | 3 | chrX | NT_011657 | AL627245 | 34541542 | 3 | 22795 | 0 | 0 | 22795 |
| S/G/Y/R/B/O |
NT_011657 | AL627245 | 34541542 | 3 | chrX | NT_011657 | AL121578 | 34636640 | 3 | 40034 | 0 | 0 | 40034 |
| S/G/Y/R/B/O |
NT_011657 | AL121578 | 34636640 | 3 | chrX | NT_011657 | AL627246 | 34933691 | 3 | 0 | 0 | 189 | 189 |
| S/G/Y/R/B/O |
NT_011657 | AL627246 | 34933691 | 3 | chrX | NT_011657 | AL133494 | 34939657 | 3 | 0 | 0 | 298 | 298 |
| S/G/Y/R/B/O |
NT_011657 | AL133494 | 34939657 | 3 | chrX | NT_011657 | AL606748 | 34977570 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011657 | AL606748 | 34977570 | 3 | chrX | NT_011657 | AL607040 | 35117147 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011657 | AL606748 | 34977570 | 3 |   |   | AJ318463 | 34933691 | 3 | 77222 | 0 | 0 | 77222 |
| S/G/Y/R/B/O |
NT_011657 | AL606748 | 34977570 | 3 |   |   | AL627412 | 34933691 | 1 | 137186 | 0 | 0 | 137186 |
| S/G/Y/R/B/O |
NT_011657 | AL606748 | 34977570 | 3 |   |   | X94768 | 34933691 | 3 | 18365 | 0 | 0 | 18365 |
| S/G/Y/R/B/O |
NT_011657 | AL607040 | 35117147 | 3 | chrX | NT_011657 | AF241726 | 35145147 | 3 | 2000 | 0 | 0 | 2000 |
| S/G/Y/R/B/O |
NT_011657 | AL607040 | 35117147 | 3 |   |   | AL627412 | 35145147 | 1 | 25683 | 0 | 0 | 25683 |
| S/G/Y/R/B/O |
NT_011657 | AF241726 | 35145147 | 3 | chrX | NT_011657 | AF241727 | 35388125 | 3 | 56796 | 0 | 0 | 56796 |
| S/G/Y/R/B/O |
NT_011657 | AF241727 | 35388125 | 3 | chrX | NT_011657 | AF241728 | 35486485 | 3 | 35801 | 0 | 0 | 35801 |
| S/G/Y/R/B/O |
NT_011657 | AF241728 | 35486485 | 3 | chrX | NT_011657 | AF241729 | 35584192 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011657 | AF241728 | 35486485 | 3 |   |   | AC022212 | 35486485 | 3 | 99469 | 0 | 0 | 99469 |
| S/G/Y/R/B/O |
NT_011657 | AF241729 | 35584192 | 3 | chrX | NT_011657 | AF241730 | 35699932 | 3 | 6048 | 0 | 0 | 6048 |
| S/G/Y/R/B/O |
NT_011657 | AF241729 | 35584192 | 3 |   |   | AC022212 | 35388125 | 3 | 113533 | 0 | 0 | 113533 |
| S/G/Y/R/B/O |
NT_011657 | AF241730 | 35699932 | 3 | chrX | NT_011657 | AF241731 | 35822312 | 3 | 22103 | 0 | 0 | 22103 |
| S/G/Y/R/B/O |
NT_011657 | AF241731 | 35822312 | 3 | chrX | NT_011657 | AF241732 | 35845171 | 3 | 26019 | 0 | 0 | 26019 |
| S/G/Y/R/B/O |
NT_011657 | AF241732 | 35845171 | 3 | chrX | NT_011657 | AF241733 | 35862048 | 3 | 9227 | 0 | 0 | 9227 |
| S/G/Y/R/B/O |
NT_011657 | AF241733 | 35862048 | 3 | chrX | NT_011657 | AC108879 | 35985981 | 3 | 99298 | 0 | 0 | 99298 |
| S/G/Y/R/B/O |
NT_011657 | AF241733 | 35862048 | 3 |   |   | AF282856 | 35845171 | 3 | 45273 | 0 | 0 | 45273 |
| S/G/Y/R/B/O |
NT_011657 | AC108879 | 35985981 | 3 | chrX | NT_011657 | AC091808 | 36111086 | 3 | 90646 | 0 | 0 | 90646 |
| S/G/Y/R/B/O |
NT_011657 | AC091808 | 36111086 | 3 | chrX | NT_011657 | AC108880 | 36235982 | 3 | 223648 | 0 | 0 | 223648 |
| S/G/Y/R/B/O |
NT_011657 | AC091808 | 36111086 | 3 |   |   | AL590090 | 36235982 | 1 | 137473 | 0 | 0 | 137473 |
| S/G/Y/R/B/O |
NT_011657 | AC108880 | 36235982 | 3 | chrX | NT_011657 | AC108881 | 36342535 | 3 | 257376 | 0 | 0 | 257376 |
| S/G/Y/R/B/O |
NT_011657 | AC108880 | 36235982 | 3 |   |   | AL590090 | 36342535 | 1 | 119236 | 0 | 0 | 119236 |
| S/G/Y/R/B/O |
NT_011657 | AC108881 | 36342535 | 3 | chrX | NT_011657 | AF241734 | 36441367 | 3 | 157484 | 0 | 0 | 157484 |
| S/G/Y/R/B/O |
NT_011657 | AC108881 | 36342535 | 3 |   |   | AC013798 | 36342535 | 1 | 56657 | 5158 | 18430 | 80245 |
| S/G/Y/R/B/O |
NT_011657 | AC108881 | 36342535 | 3 |   |   | AL670662 | 36441367 | 2 | 231372 | 0 | 0 | 231372 |
| S/G/Y/R/B/O |
NT_011657 | AF241734 | 36441367 | 3 | chrX | NT_011657 | AC091810 | 36482510 | 3 | 13313 | 0 | 0 | 13313 |
| S/G/Y/R/B/O |
NT_011657 | AF241734 | 36441367 | 3 |   |   | AC013798 | 36441367 | 1 | 81389 | 5011 | 8890 | 95290 |
| S/G/Y/R/B/O |
NT_011657 | AF241734 | 36441367 | 3 |   |   | AC115573 | 36342535 | 3 | 13313 | 0 | 0 | 13313 |
| S/G/Y/R/B/O |
NT_011657 | AF241734 | 36441367 | 3 |   |   | AL670662 | 36342535 | 2 | 78741 | 0 | 0 | 78741 |
| S/G/Y/R/B/O |
NT_011657 | AC091810 | 36482510 | 3 | chrX | NT_011657 | AL592164 | 36569651 | 3 | 2000 | 0 | 0 | 2000 |
| S/G/Y/R/B/O |
NT_011657 | AC091810 | 36482510 | 3 |   |   | AC013798 | 36342535 | 1 | 66777 | 0 | 0 | 66777 |
| S/G/Y/R/B/O |
NT_011657 | AC091810 | 36482510 | 3 |   |   | AC115573 | 36342535 | 3 | 100473 | 0 | 0 | 100473 |
| S/G/Y/R/B/O |
NT_011657 | AC091810 | 36482510 | 3 |   |   | AF241735 | 36441367 | 3 | 39834 | 0 | 0 | 39834 |
| S/G/Y/R/B/O |
NT_011657 | AL592164 | 36569651 | 3 | chrX | NT_011657 | AC092198 | 36692308 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011657 | AL592164 | 36569651 | 3 |   |   | AL590292 | 36482510 | 1 | 80762 | 0 | 0 | 80762 |
| S/G/Y/R/B/O |
NT_011657 | AC092198 | 36692308 | 3 | chrX | NT_011657 | AL591802 | 36850173 | 3 | 67259 | 0 | 0 | 67259 |
| S/G/Y/R/B/O |
NT_011657 | AC092198 | 36692308 | 3 |   |   | AC091809 | 170600520 | 3 | 14851 | 0 | 0 | 14851 |
| S/G/Y/R/B/O |
NT_011657 | AC092198 | 36692308 | 3 |   |   | AL590292 | 170600520 | 1 | 70366 | 0 | 20598 | 90964 |
| S/G/Y/R/B/O |
NT_011657 | AL591802 | 36850173 | 3 | chrX | NT_011657 | AC091806 | 36985163 | 3 | 81989 | 0 | 0 | 81989 |
| S/G/Y/R/B/O |
NT_011657 | AL591802 | 36850173 | 3 | chr17 | NT_024857 | AC104342 | 8514844 | 2 | 65629 | 0 | 24990 | 90619 |
| S/G/Y/R/B/O |
NT_011657 | AL591802 | 36850173 | 3 |   |   | AC091809 | 36985163 | 3 | 149730 | 0 | 0 | 149730 |
| S/G/Y/R/B/O |
NT_011657 | AC091806 | 36985163 | 3 | chrX | NT_011657 | AC091807 | 37085883 | 3 | 0 | 0 | 348 | 348 |
| S/G/Y/R/B/O |
NT_011657 | AC091806 | 36985163 | 3 | chr17 | NT_024857 | AC027551 | 8528802 | 1 | 49852 | 2381 | 0 | 52233 |
| S/G/Y/R/B/O |
NT_011657 | AC091806 | 36985163 | 3 | chr17 | NT_024857 | AC069362 | 8538699 | 3 | 11930 | 0 | 0 | 11930 |
| S/G/Y/R/B/O |
NT_011657 | AC091806 | 36985163 | 3 | chr17 | NT_024857 | AC104342 | 8514844 | 2 | 85511 | 0 | 4599 | 90110 |
| S/G/Y/R/B/O |
NT_011657 | AC091806 | 36985163 | 3 |   |   | AC091809 | 37085883 | 3 | 150156 | 0 | 0 | 150156 |
| S/G/Y/R/B/O |
NT_011657 | AC091807 | 37085883 | 3 | chrX | NT_011657 | AC092473 | 37257685 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011657 | AC091807 | 37085883 | 3 | chr17 | NT_024857 | AC027551 | 8528802 | 1 | 80191 | 2426 | 0 | 82617 |
| S/G/Y/R/B/O |
NT_011657 | AC091807 | 37085883 | 3 | chr17 | NT_024857 | AC069362 | 8538699 | 3 | 164565 | 0 | 0 | 164565 |
| S/G/Y/R/B/O |
NT_011657 | AC091807 | 37085883 | 3 |   |   | AL592165 | 145589636 | 1 | 62878 | 2689 | 34096 | 99663 |
| S/G/Y/R/B/O |
NT_011657 | AC092473 | 37257685 | 3 | chrX | NT_011657 | AC093029 | 37395350 | 1 | 31110 | 0 | 0 | 31110 |
| S/G/Y/R/B/O |
NT_011657 | AC092473 | 37257685 | 3 |   |   | AC026156 | 145589636 | 1 | 56847 | 0 | 0 | 56847 |
| S/G/Y/R/B/O |
NT_011657 | AC093029 | 37395350 | 1 |   |   |   |   |   |   |   |   |   |
| S/G/Y/R/B/O |
NT_011657 | AC093029 | 37395350 | 1 |   |   | AC026156 | 37395350 | 1 | 14336 | 1800 | 1018 | 17154 |
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