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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_006519 | AC016155 | 188295236 | 1 | chr5 | NT_006519 | AC104115 | 188364200 | 2 | 89203 | 2972 | 2716 | 94891 |
| S/G/Y/R/B/O |
NT_006519 | AC016155 | 188295236 | 1 | chr5 | NT_006519 | AC092290 | 188425154 | 3 | 18076 | 0 | 0 | 18076 |
| S/G/Y/R/B/O |
NT_006519 | AC104115 | 188364200 | 2 | chr5 | NT_006519 | AC092290 | 188425154 | 3 | 77657 | 0 | 0 | 77657 |
| S/G/Y/R/B/O |
NT_006519 | AC104115 | 188364200 | 2 | chr5 | NT_006519 | AC106766 | 188492448 | 1 | 28538 | 2975 | 0 | 31513 |
| S/G/Y/R/B/O |
NT_006519 | AC104115 | 188364200 | 2 |   |   | AC008610 | 188364200 | 3 | 38719 | 2969 | 0 | 41688 |
| S/G/Y/R/B/O |
NT_006519 | AC092290 | 188425154 | 3 | chr5 | NT_006519 | AC106766 | 188492448 | 1 | 0 | 0 | 21387 | 21387 |
| S/G/Y/R/B/O |
NT_006519 | AC092290 | 188425154 | 3 | chr5 | NT_006519 | AC016155 | 188295236 | 1 | 18076 | 0 | 0 | 18076 |
| S/G/Y/R/B/O |
NT_006519 | AC092290 | 188425154 | 3 |   |   | AC008610 | 188492448 | 3 | 39812 | 0 | 0 | 39812 |
| S/G/Y/R/B/O |
NT_006519 | AC106766 | 188492448 | 1 | chr5 | NT_006519 | AC034213 | 188598547 | 3 | 19070 | 0 | 0 | 19070 |
| S/G/Y/R/B/O |
NT_006519 | AC106766 | 188492448 | 1 | chr5 | NT_006519 | AC104115 | 188364200 | 2 | 28538 | 2975 | 0 | 31513 |
| S/G/Y/R/B/O |
NT_006519 | AC106766 | 188492448 | 1 |   |   | AC008610 | 188492448 | 3 | 90792 | 0 | 19676 | 110468 |
| S/G/Y/R/B/O |
NT_006519 | AC034213 | 188598547 | 3 | chr5 | NT_006519 | AC110000 | 188740556 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_006519 | AC034213 | 188598547 | 3 | chr5 | NT_006519 | AC022095 | 188862110 | 1 | 21163 | 0 | 0 | 21163 |
| S/G/Y/R/B/O |
NT_006519 | AC034213 | 188598547 | 3 | chr5 | NT_006519 | AC025336 | 188832249 | 1 | 26379 | 0 | 1473 | 27852 |
| S/G/Y/R/B/O |
NT_006519 | AC034213 | 188598547 | 3 |   |   | AC108083 | 188492448 | 1 | 37078 | 0 | 0 | 37078 |
| S/G/Y/R/B/O |
NT_006519 | AC110000 | 188740556 | 3 | chr5 | NT_006519 | AC106813 | 188776984 | 2 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_006519 | AC110000 | 188740556 | 3 | chr5 | NT_006519 | AC025336 | 188832249 | 1 | 20101 | 1786 | 1389 | 23276 |
| S/G/Y/R/B/O |
NT_006519 | AC110000 | 188740556 | 3 |   |   | AC108083 | 188832249 | 1 | 36428 | 0 | 0 | 36428 |
| S/G/Y/R/B/O |
NT_006519 | AC106813 | 188776984 | 2 | chr5 | NT_006519 | AC025336 | 188832249 | 1 | 105475 | 11046 | 1389 | 117910 |
| S/G/Y/R/B/O |
NT_006519 | AC106813 | 188776984 | 2 | chr5 | NT_006519 | AC022095 | 188862110 | 1 | 80644 | 2448 | 7712 | 90804 |
| S/G/Y/R/B/O |
NT_006519 | AC106813 | 188776984 | 2 | chr5 | NT_006519 | AC023255 | 188839869 | 1 | 27246 | 0 | 0 | 27246 |
| S/G/Y/R/B/O |
NT_006519 | AC106813 | 188776984 | 2 | chr5 | NT_006519 | AC113427 | 188852802 | 1 | 27254 | 0 | 0 | 27254 |
| S/G/Y/R/B/O |
NT_006519 | AC025336 | 188832249 | 1 | chr5 | NT_006519 | AC023255 | 188839869 | 1 | 11108 | 0 | 0 | 11108 |
| S/G/Y/R/B/O |
NT_006519 | AC025336 | 188832249 | 1 | chr5 | NT_006519 | AC022095 | 188862110 | 1 | 44888 | 7828 | 17552 | 70268 |
| S/G/Y/R/B/O |
NT_006519 | AC025336 | 188832249 | 1 | chr5 | NT_006519 | AC034213 | 188598547 | 3 | 26379 | 0 | 1473 | 27852 |
| S/G/Y/R/B/O |
NT_006519 | AC025336 | 188832249 | 1 | chr5 | NT_006519 | AC110000 | 188740556 | 3 | 20101 | 1786 | 1389 | 23276 |
| S/G/Y/R/B/O |
NT_006519 | AC025336 | 188832249 | 1 | chr5 | NT_006519 | AC113427 | 188852802 | 1 | 11112 | 0 | 0 | 11112 |
| S/G/Y/R/B/O |
NT_006519 | AC025336 | 188832249 | 1 |   |   | AC108083 | 188776984 | 1 | 74270 | 7823 | 6761 | 88854 |
| S/G/Y/R/B/O |
NT_006519 | AC023255 | 188839869 | 1 | chr5 | NT_006519 | AC113427 | 188852802 | 1 | 111080 | 5473 | 0 | 116553 |
| S/G/Y/R/B/O |
NT_006519 | AC023255 | 188839869 | 1 | chr5 | NT_006519 | AC016572 | 189159095 | 3 | 16426 | 2525 | 0 | 18951 |
| S/G/Y/R/B/O |
NT_006519 | AC023255 | 188839869 | 1 | chr5 | NT_006519 | AC022413 | 189016268 | 3 | 76106 | 2532 | 0 | 78638 |
| S/G/Y/R/B/O |
NT_006519 | AC023255 | 188839869 | 1 | chr5 | NT_006519 | AC106813 | 188776984 | 2 | 27246 | 0 | 0 | 27246 |
| S/G/Y/R/B/O |
NT_006519 | AC023255 | 188839869 | 1 | chr5 | NT_006519 | AC106823 | 188955939 | 3 | 53359 | 2940 | 0 | 56299 |
| S/G/Y/R/B/O |
NT_006519 | AC113427 | 188852802 | 1 | chr5 | NT_006519 | AC022095 | 188862110 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_006519 | AC113427 | 188852802 | 1 | chr5 | NT_006519 | AC022413 | 189016268 | 3 | 99933 | 0 | 741 | 100674 |
| S/G/Y/R/B/O |
NT_006519 | AC113427 | 188852802 | 1 | chr5 | NT_006519 | AC025336 | 188832249 | 1 | 11112 | 0 | 0 | 11112 |
| S/G/Y/R/B/O |
NT_006519 | AC113427 | 188852802 | 1 | chr5 | NT_006519 | AC106813 | 188776984 | 2 | 27254 | 0 | 0 | 27254 |
| S/G/Y/R/B/O |
NT_006519 | AC113427 | 188852802 | 1 | chr5 | NT_006519 | AC106823 | 188955939 | 3 | 60329 | 0 | 0 | 60329 |
| S/G/Y/R/B/O |
NT_006519 | AC022095 | 188862110 | 1 | chr5 | NT_006519 | AC106823 | 188955939 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_006519 | AC022095 | 188862110 | 1 | chr5 | NT_006519 | AC025336 | 188832249 | 1 | 44888 | 7828 | 17552 | 70268 |
| S/G/Y/R/B/O |
NT_006519 | AC022095 | 188862110 | 1 | chr5 | NT_006519 | AC034213 | 188598547 | 3 | 21163 | 0 | 0 | 21163 |
| S/G/Y/R/B/O |
NT_006519 | AC022095 | 188862110 | 1 | chr5 | NT_006519 | AC106813 | 188776984 | 2 | 80644 | 2448 | 7712 | 90804 |
| S/G/Y/R/B/O |
NT_006519 | AC022095 | 188862110 | 1 |   |   | AC108083 | 188776984 | 1 | 35663 | 2448 | 50870 | 88981 |
| S/G/Y/R/B/O |
NT_006519 | AC106823 | 188955939 | 3 | chr5 | NT_006519 | AC022413 | 189016268 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_006519 | AC106823 | 188955939 | 3 | chr5 | NT_006519 | AC023255 | 188839869 | 1 | 53359 | 2940 | 0 | 56299 |
| S/G/Y/R/B/O |
NT_006519 | AC106823 | 188955939 | 3 | chr5 | NT_006519 | AC113427 | 188852802 | 1 | 60329 | 0 | 0 | 60329 |
| S/G/Y/R/B/O |
NT_006519 | AC022413 | 189016268 | 3 | chr5 | NT_006519 | AC016572 | 189159095 | 3 | 85501 | 0 | 0 | 85501 |
| S/G/Y/R/B/O |
NT_006519 | AC022413 | 189016268 | 3 | chr5 | NT_006519 | AC023255 | 188839869 | 1 | 76106 | 2532 | 0 | 78638 |
| S/G/Y/R/B/O |
NT_006519 | AC022413 | 189016268 | 3 | chr5 | NT_006519 | AC113427 | 188852802 | 1 | 99933 | 0 | 741 | 100674 |
| S/G/Y/R/B/O |
NT_006519 | AC016572 | 189159095 | 3 | chr5 | NT_006519 | AC091874 | 189217135 | 2 | 65665 | 0 | 0 | 65665 |
| S/G/Y/R/B/O |
NT_006519 | AC016572 | 189159095 | 3 | chr5 | NT_006519 | AC023255 | 188839869 | 1 | 16426 | 2525 | 0 | 18951 |
| S/G/Y/R/B/O |
NT_006519 | AC091874 | 189217135 | 2 | chr5 | NT_006519 | AC008620 | 189297730 | 2 | 0 | 1232 | 0 | 1232 |
| S/G/Y/R/B/O |
NT_006519 | AC008620 | 189297730 | 2 | chr5 | NT_006519 | AC008443 | 189413452 | 3 | 66797 | 0 | 0 | 66797 |
| S/G/Y/R/B/O |
NT_006519 | AC008620 | 189297730 | 2 |   |   | AL161615 | 152276364 | 1 | 52963 | 3446 | 3565 | 59974 |
| S/G/Y/R/B/O |
NT_006519 | AC008443 | 189413452 | 3 |   |   |   |   |   |   |   |   |   |
| S/G/Y/R/B/O |
NT_006519 | AC008443 | 189413452 | 3 |   |   | AL161615 | 152276364 | 1 | 64825 | 7548 | 8985 | 81358 |
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