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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_011726 | AF002992 | 146953668 | 3 | chrX | NT_011726 | AF274855 | 147057705 | 3 | 0 | 0 | 249 | 249 |
| S/G/Y/R/B/O |
NT_011726 | AF274855 | 147057705 | 3 | chrX | NT_011726 | U82696 | 147107471 | 3 | 0 | 0 | 250 | 250 |
| S/G/Y/R/B/O |
NT_011726 | U82696 | 147107471 | 3 | chrX | NT_011726 | AF274856 | 147266119 | 3 | 63122 | 0 | 0 | 63122 |
| S/G/Y/R/B/O |
NT_011726 | AF274856 | 147266119 | 3 | chrX | NT_011726 | AF134576 | 147376781 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011726 | AF274856 | 147266119 | 3 | chrX | NT_011726 | AC009621 | 147520039 | 1 | 16857 | 2032 | 14350 | 33239 |
| S/G/Y/R/B/O |
NT_011726 | AF274856 | 147266119 | 3 | chrX | NT_011726 | AC024727 | 147521283 | 1 | 42021 | 0 | 15708 | 57729 |
| S/G/Y/R/B/O |
NT_011726 | AF274856 | 147266119 | 3 | chrX | NT_011726 | AC116666 | 147408429 | 3 | 66557 | 0 | 0 | 66557 |
| S/G/Y/R/B/O |
NT_011726 | AF134576 | 147376781 | 3 | chrX | NT_011726 | AC116666 | 147408429 | 3 | 66498 | 0 | 0 | 66498 |
| S/G/Y/R/B/O |
NT_011726 | AF134576 | 147376781 | 3 | chrX | NT_011726 | AC009621 | 147520039 | 1 | 45656 | 4024 | 6882 | 56562 |
| S/G/Y/R/B/O |
NT_011726 | AF134576 | 147376781 | 3 | chrX | NT_011726 | AC024727 | 147521283 | 1 | 48196 | 0 | 6849 | 55045 |
| S/G/Y/R/B/O |
NT_011726 | AC116666 | 147408429 | 3 | chrX | NT_011726 | AF282854 | 147479389 | 1 | 37274 | 0 | 0 | 37274 |
| S/G/Y/R/B/O |
NT_011726 | AC116666 | 147408429 | 3 | chrX | NT_011726 | AC009621 | 147520039 | 1 | 110086 | 8472 | 13256 | 131814 |
| S/G/Y/R/B/O |
NT_011726 | AC116666 | 147408429 | 3 | chrX | NT_011726 | AC024727 | 147521283 | 1 | 129510 | 3739 | 23740 | 156989 |
| S/G/Y/R/B/O |
NT_011726 | AC116666 | 147408429 | 3 | chrX | NT_011726 | AF274856 | 147266119 | 3 | 66557 | 0 | 0 | 66557 |
| S/G/Y/R/B/O |
NT_011726 | AF282854 | 147479389 | 1 | chrX | NT_011726 | AC009621 | 147520039 | 1 | 51082 | 2412 | 2295 | 55789 |
| S/G/Y/R/B/O |
NT_011726 | AF282854 | 147479389 | 1 | chrX | NT_011726 | AC024727 | 147521283 | 1 | 31926 | 0 | 0 | 31926 |
| S/G/Y/R/B/O |
NT_011726 | AF282854 | 147479389 | 1 | chr14 | NT_026437 | AC024931 | 93352801 | 1 | 79325 | 0 | 31426 | 110751 |
| S/G/Y/R/B/O |
NT_011726 | AF282854 | 147479389 | 1 | chrX | NT_011726 | AF036938 | 147582788 | 3 | 39437 | 0 | 0 | 39437 |
| S/G/Y/R/B/O |
NT_011726 | AF282854 | 147479389 | 1 | chrX | NT_011726 | AF274857 | 147622232 | 3 | 19190 | 0 | 0 | 19190 |
| S/G/Y/R/B/O |
NT_011726 | AC009621 | 147520039 | 1 | chrX | NT_011726 | AC024727 | 147521283 | 1 | 49891 | 3739 | 4673 | 58303 |
| S/G/Y/R/B/O |
NT_011726 | AC009621 | 147520039 | 1 | chr14 | NT_026437 | AC024931 | 93352801 | 1 | 11561 | 0 | 0 | 11561 |
| S/G/Y/R/B/O |
NT_011726 | AC009621 | 147520039 | 1 | chrX | NT_011726 | AC116666 | 147408429 | 3 | 110086 | 8472 | 13256 | 131814 |
| S/G/Y/R/B/O |
NT_011726 | AC009621 | 147520039 | 1 | chrX | NT_011726 | AF134576 | 147376781 | 3 | 45656 | 4024 | 6882 | 56562 |
| S/G/Y/R/B/O |
NT_011726 | AC009621 | 147520039 | 1 | chrX | NT_011726 | AF274856 | 147266119 | 3 | 16857 | 2032 | 14350 | 33239 |
| S/G/Y/R/B/O |
NT_011726 | AC024727 | 147521283 | 1 | chrX | NT_011726 | AF036938 | 147582788 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011726 | AC024727 | 147521283 | 1 | chrX | NT_011726 | AC116666 | 147408429 | 3 | 129510 | 3739 | 23740 | 156989 |
| S/G/Y/R/B/O |
NT_011726 | AC024727 | 147521283 | 1 | chrX | NT_011726 | AF134576 | 147376781 | 3 | 48196 | 0 | 6849 | 55045 |
| S/G/Y/R/B/O |
NT_011726 | AC024727 | 147521283 | 1 | chrX | NT_011726 | AF274856 | 147266119 | 3 | 42021 | 0 | 15708 | 57729 |
| S/G/Y/R/B/O |
NT_011726 | AC024727 | 147521283 | 1 | chrX | NT_011726 | AF282854 | 147479389 | 1 | 31926 | 0 | 0 | 31926 |
| S/G/Y/R/B/O |
NT_011726 | AF036938 | 147582788 | 3 | chrX | NT_011726 | AF274857 | 147622232 | 3 | 8902 | 0 | 0 | 8902 |
| S/G/Y/R/B/O |
NT_011726 | AF036938 | 147582788 | 3 | chr14 | NT_026437 | AC024931 | 93352801 | 1 | 29999 | 0 | 0 | 29999 |
| S/G/Y/R/B/O |
NT_011726 | AF036938 | 147582788 | 3 | chrX | NT_011726 | AF282854 | 147479389 | 1 | 39437 | 0 | 0 | 39437 |
| S/G/Y/R/B/O |
NT_011726 | AF274857 | 147622232 | 3 | chrX | NT_011726 | AC108171 | 147761850 | 3 | 0 | 1994 | 0 | 1994 |
| S/G/Y/R/B/O |
NT_011726 | AF274857 | 147622232 | 3 | chrX | NT_011726 | AF282854 | 147479389 | 1 | 19190 | 0 | 0 | 19190 |
| S/G/Y/R/B/O |
NT_011726 | AC108171 | 147761850 | 3 | chrX | NT_011726 | AF002997 | 147786659 | 3 | 2000 | 0 | 0 | 2000 |
| S/G/Y/R/B/O |
NT_011726 | AF002997 | 147786659 | 3 | chrX | NT_011726 | U82671 | 148029736 | 3 | 70766 | 0 | 0 | 70766 |
| S/G/Y/R/B/O |
NT_011726 | AF002997 | 147786659 | 3 |   |   | AF002994 | 147761850 | 3 | 54007 | 0 | 0 | 54007 |
| S/G/Y/R/B/O |
NT_011726 | AF002997 | 147786659 | 3 |   |   | AF030261 | 147761850 | 3 | 75258 | 0 | 0 | 75258 |
| S/G/Y/R/B/O |
NT_011726 | U82671 | 148029736 | 3 | chrX | NT_011726 | U82670 | 148248114 | 3 | 0 | 0 | 250 | 250 |
| S/G/Y/R/B/O |
NT_011726 | U82671 | 148029736 | 3 |   |   | AC093682 | 148029736 | 1 | 35461 | 16041 | 20690 | 72192 |
| S/G/Y/R/B/O |
NT_011726 | U82671 | 148029736 | 3 |   |   | AF002995 | 148029736 | 3 | 43973 | 0 | 0 | 43973 |
| S/G/Y/R/B/O |
NT_011726 | U82671 | 148029736 | 3 |   |   | AF002996 | 148029736 | 3 | 35554 | 0 | 0 | 35554 |
| S/G/Y/R/B/O |
NT_011726 | U82671 | 148029736 | 3 |   |   | AF006487 | 147786659 | 3 | 36860 | 0 | 0 | 36860 |
| S/G/Y/R/B/O |
NT_011726 | U82671 | 148029736 | 3 |   |   | AF027974 | 147786659 | 3 | 45320 | 0 | 0 | 45320 |
| S/G/Y/R/B/O |
NT_011726 | U82671 | 148029736 | 3 |   |   | AF030261 | 147786659 | 3 | 37758 | 0 | 0 | 37758 |
| S/G/Y/R/B/O |
NT_011726 | U82670 | 148248114 | 3 |   |   |   |   |   |   |   |   |   |
| S/G/Y/R/B/O |
NT_011726 | U82670 | 148248114 | 3 |   |   | U82672 | 148029736 | 3 | 156733 | 0 | 0 | 156733 |
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