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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_009743 | AC093024 | 101316541 | 1 | chr12 | NT_009743 | AC022290 | 101317029 | 1 | 56547 | 12343 | 15748 | 84638 |
| S/G/Y/R/B/O |
NT_009743 | AC093024 | 101316541 | 1 | chr12 | NT_009743 | AC021053 | 102225080 | 1 | 10021 | 4553 | 0 | 14574 |
| S/G/Y/R/B/O |
NT_009743 | AC093024 | 101316541 | 1 | chr12 | NT_009743 | AC026615 | 101408356 | 1 | 35223 | 8980 | 1242 | 45445 |
| S/G/Y/R/B/O |
NT_009743 | AC093024 | 101316541 | 1 | chr12 | NT_009743 | AC090671 | 101418835 | 1 | 30073 | 0 | 2491 | 32564 |
| S/G/Y/R/B/O |
NT_009743 | AC022290 | 101317029 | 1 | chr12 | NT_009743 | AC063948 | 101322306 | 1 | 38066 | 4781 | 13606 | 56453 |
| S/G/Y/R/B/O |
NT_009743 | AC022290 | 101317029 | 1 | chr12 | NT_009743 | AC021053 | 102225080 | 1 | 21233 | 4661 | 1228 | 27122 |
| S/G/Y/R/B/O |
NT_009743 | AC022290 | 101317029 | 1 | chr12 | NT_009743 | AC026615 | 101408356 | 1 | 35417 | 6148 | 14096 | 55661 |
| S/G/Y/R/B/O |
NT_009743 | AC022290 | 101317029 | 1 | chr12 | NT_009743 | AC090671 | 101418835 | 1 | 35268 | 0 | 0 | 35268 |
| S/G/Y/R/B/O |
NT_009743 | AC022290 | 101317029 | 1 |   |   | AC026549 | 102225080 | 1 | 15575 | 17092 | 2291 | 34958 |
| S/G/Y/R/B/O |
NT_009743 | AC063948 | 101322306 | 1 | chr12 | NT_009743 | AC026615 | 101408356 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009743 | AC063948 | 101322306 | 1 | chr12 | NT_009743 | AC021053 | 102225080 | 1 | 97553 | 2554 | 5213 | 105320 |
| S/G/Y/R/B/O |
NT_009743 | AC063948 | 101322306 | 1 |   |   | AC026549 | 101317029 | 1 | 99842 | 14409 | 14837 | 129088 |
| S/G/Y/R/B/O |
NT_009743 | AC026615 | 101408356 | 1 | chr12 | NT_009743 | AC090671 | 101418835 | 1 | 71406 | 7059 | 8206 | 86671 |
| S/G/Y/R/B/O |
NT_009743 | AC026615 | 101408356 | 1 | chr12 | NT_009743 | AC022290 | 101317029 | 1 | 35417 | 6148 | 14096 | 55661 |
| S/G/Y/R/B/O |
NT_009743 | AC026615 | 101408356 | 1 | chr12 | NT_009743 | AC073833 | 101429327 | 1 | 70929 | 1069 | 3645 | 75643 |
| S/G/Y/R/B/O |
NT_009743 | AC026615 | 101408356 | 1 | chr12 | NT_009743 | AC093024 | 101316541 | 1 | 35223 | 8980 | 1242 | 45445 |
| S/G/Y/R/B/O |
NT_009743 | AC090671 | 101418835 | 1 | chr12 | NT_009743 | AC073833 | 101429327 | 1 | 66514 | 0 | 3392 | 69906 |
| S/G/Y/R/B/O |
NT_009743 | AC090671 | 101418835 | 1 | chr12 | NT_009743 | AC022290 | 101317029 | 1 | 35268 | 0 | 0 | 35268 |
| S/G/Y/R/B/O |
NT_009743 | AC090671 | 101418835 | 1 | chr12 | NT_009743 | AC093024 | 101316541 | 1 | 30073 | 0 | 2491 | 32564 |
| S/G/Y/R/B/O |
NT_009743 | AC073833 | 101429327 | 1 | chr12 | NT_009743 | AC010205 | 101595353 | 3 | 21337 | 1584 | 12521 | 35442 |
| S/G/Y/R/B/O |
NT_009743 | AC073833 | 101429327 | 1 | chr12 | NT_009743 | AC026615 | 101408356 | 1 | 70929 | 1069 | 3645 | 75643 |
| S/G/Y/R/B/O |
NT_009743 | AC073833 | 101429327 | 1 | chrX | NT_011754 | AC079264 | 15586615 | 3 | 19824 | 10034 | 24890 | 54748 |
| S/G/Y/R/B/O |
NT_009743 | AC073833 | 101429327 | 1 |   |   | AC015503 | 101595353 | 1 | 11382 | 0 | 5518 | 16900 |
| S/G/Y/R/B/O |
NT_009743 | AC073833 | 101429327 | 1 |   |   | AC055112 | 101408356 | 1 | 14908 | 12501 | 34469 | 61878 |
| S/G/Y/R/B/O |
NT_009743 | AC010205 | 101595353 | 3 | chr12 | NT_009743 | AC005409 | 101757780 | 3 | 120092 | 0 | 0 | 120092 |
| S/G/Y/R/B/O |
NT_009743 | AC010205 | 101595353 | 3 | chr12 | NT_009743 | AC063950 | 101814983 | 3 | 113782 | 0 | 0 | 113782 |
| S/G/Y/R/B/O |
NT_009743 | AC005409 | 101757780 | 3 | chr12 | NT_009743 | AC063950 | 101814983 | 3 | 171003 | 0 | 0 | 171003 |
| S/G/Y/R/B/O |
NT_009743 | AC063950 | 101814983 | 3 | chr12 | NT_009743 | AC084398 | 101818162 | 1 | 5160 | 0 | 10915 | 16075 |
| S/G/Y/R/B/O |
NT_009743 | AC063950 | 101814983 | 3 | chr12 | NT_009743 | AC010205 | 101595353 | 3 | 113782 | 0 | 0 | 113782 |
| S/G/Y/R/B/O |
NT_009743 | AC084398 | 101818162 | 1 | chr12 | NT_009743 | AC079907 | 101859505 | 3 | 4541 | 0 | 0 | 4541 |
| S/G/Y/R/B/O |
NT_009743 | AC079907 | 101859505 | 3 | chr12 | NT_009743 | AC036229 | 102044345 | 1 | 46652 | 1651 | 0 | 48303 |
| S/G/Y/R/B/O |
NT_009743 | AC079907 | 101859505 | 3 | chr12 | NT_009743 | AC087882 | 102050372 | 1 | 11387 | 0 | 4994 | 16381 |
| S/G/Y/R/B/O |
NT_009743 | AC036229 | 102044345 | 1 | chr12 | NT_009743 | AC087882 | 102050372 | 1 | 34320 | 5866 | 25521 | 65707 |
| S/G/Y/R/B/O |
NT_009743 | AC036229 | 102044345 | 1 | chr12 | NT_009743 | AC093023 | 102124329 | 1 | 24398 | 0 | 3118 | 27516 |
| S/G/Y/R/B/O |
NT_009743 | AC087882 | 102050372 | 1 | chr12 | NT_009743 | AC093023 | 102124329 | 1 | 4068 | 0 | 1907 | 5975 |
| S/G/Y/R/B/O |
NT_009743 | AC087882 | 102050372 | 1 | chr12 | NT_009743 | AC079907 | 101859505 | 3 | 11387 | 0 | 4994 | 16381 |
| S/G/Y/R/B/O |
NT_009743 | AC093023 | 102124329 | 1 | chr12 | NT_009743 | AC021053 | 102225080 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009743 | AC093023 | 102124329 | 1 | chr12 | NT_009743 | AC036229 | 102044345 | 1 | 24398 | 0 | 3118 | 27516 |
| S/G/Y/R/B/O |
NT_009743 | AC093023 | 102124329 | 1 | chr12 | NT_009743 | AC068648 | 103104904 | 3 | 107964 | 0 | 18299 | 126263 |
| S/G/Y/R/B/O |
NT_009743 | AC021053 | 102225080 | 1 | chr12 | NT_009743 | AC063951 | 102256294 | 3 | 52622 | 0 | 0 | 52622 |
| S/G/Y/R/B/O |
NT_009743 | AC021053 | 102225080 | 1 | chr12 | NT_009743 | AC022290 | 101317029 | 1 | 21233 | 4661 | 1228 | 27122 |
| S/G/Y/R/B/O |
NT_009743 | AC021053 | 102225080 | 1 | chr12 | NT_009743 | AC063948 | 101322306 | 1 | 97553 | 2554 | 5213 | 105320 |
| S/G/Y/R/B/O |
NT_009743 | AC021053 | 102225080 | 1 | chr12 | NT_009743 | AC093024 | 101316541 | 1 | 10021 | 4553 | 0 | 14574 |
| S/G/Y/R/B/O |
NT_009743 | AC021053 | 102225080 | 1 |   |   | AC026549 | 101317029 | 1 | 88481 | 13549 | 12867 | 114897 |
| S/G/Y/R/B/O |
NT_009743 | AC063951 | 102256294 | 3 | chr12 | NT_009743 | AC023056 | 102383478 | 1 | 111051 | 0 | 0 | 111051 |
| S/G/Y/R/B/O |
NT_009743 | AC063951 | 102256294 | 3 | chr12 | NT_009743 | AC027087 | 103817533 | 1 | 25415 | 9014 | 1386 | 35815 |
| S/G/Y/R/B/O |
NT_009743 | AC063951 | 102256294 | 3 |   |   | AC026549 | 102383478 | 1 | 21521 | 1947 | 1369 | 24837 |
| S/G/Y/R/B/O |
NT_009743 | AC063951 | 102256294 | 3 |   |   | AC058819 | 103817533 | 1 | 89930 | 8275 | 15813 | 114018 |
| S/G/Y/R/B/O |
NT_009743 | AC063951 | 102256294 | 3 |   |   | AC079953 | 103817533 | 1 | 146498 | 0 | 0 | 146498 |
| S/G/Y/R/B/O |
NT_009743 | AC023056 | 102383478 | 1 | chr12 | NT_009743 | AC063947 | 102437515 | 3 | 87009 | 0 | 0 | 87009 |
| S/G/Y/R/B/O |
NT_009743 | AC023056 | 102383478 | 1 | chr12 | NT_009743 | AC026867 | 102629296 | 1 | 18968 | 0 | 12479 | 31447 |
| S/G/Y/R/B/O |
NT_009743 | AC023056 | 102383478 | 1 | chr12 | NT_009743 | AC027087 | 103817533 | 1 | 39303 | 10722 | 5215 | 55240 |
| S/G/Y/R/B/O |
NT_009743 | AC023056 | 102383478 | 1 |   |   | AC058819 | 103817533 | 1 | 77879 | 5712 | 23821 | 107412 |
| S/G/Y/R/B/O |
NT_009743 | AC023056 | 102383478 | 1 |   |   | AC079953 | 102256294 | 1 | 118069 | 0 | 0 | 118069 |
| S/G/Y/R/B/O |
NT_009743 | AC063947 | 102437515 | 3 | chr12 | NT_009743 | AC026867 | 102629296 | 1 | 91579 | 5607 | 33610 | 130796 |
| S/G/Y/R/B/O |
NT_009743 | AC063947 | 102437515 | 3 | chr12 | NT_009743 | AC027087 | 103817533 | 1 | 45372 | 31227 | 2657 | 79256 |
| S/G/Y/R/B/O |
NT_009743 | AC026867 | 102629296 | 1 | chr12 | NT_009743 | AC010200 | 102636223 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009743 | AC026867 | 102629296 | 1 | chr12 | NT_009743 | AC023056 | 102383478 | 1 | 18968 | 0 | 12479 | 31447 |
| S/G/Y/R/B/O |
NT_009743 | AC026867 | 102629296 | 1 | chr12 | NT_009743 | AC027087 | 103817533 | 1 | 17039 | 14985 | 2938 | 34962 |
| S/G/Y/R/B/O |
NT_009743 | AC026867 | 102629296 | 1 | chr12 | NT_009743 | AC060829 | 102913242 | 1 | 18600 | 3853 | 3567 | 26020 |
| S/G/Y/R/B/O |
NT_009743 | AC010200 | 102636223 | 3 | chr12 | NT_009743 | AC010209 | 102793896 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009743 | AC010200 | 102636223 | 3 |   |   | AL157942 | 102437515 | 1 | 66886 | 1427 | 0 | 68313 |
| S/G/Y/R/B/O |
NT_009743 | AC010209 | 102793896 | 3 | chr12 | NT_009743 | AC060829 | 102913242 | 1 | 0 | 1527 | 0 | 1527 |
| S/G/Y/R/B/O |
NT_009743 | AC060829 | 102913242 | 1 | chr12 | NT_009743 | AC068648 | 103104904 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009743 | AC060829 | 102913242 | 1 | chr12 | NT_009743 | AC026867 | 102629296 | 1 | 18600 | 3853 | 3567 | 26020 |
| S/G/Y/R/B/O |
NT_009743 | AC068648 | 103104904 | 3 | chr12 | NT_009743 | AC010202 | 103231229 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009743 | AC068648 | 103104904 | 3 | chr12 | NT_009743 | AC093023 | 102124329 | 1 | 107964 | 0 | 18299 | 126263 |
| S/G/Y/R/B/O |
NT_009743 | AC010202 | 103231229 | 3 | chr12 | NT_009743 | AC021058 | 103401034 | 3 | 84112 | 0 | 0 | 84112 |
| S/G/Y/R/B/O |
NT_009743 | AC010202 | 103231229 | 3 |   |   | AC026107 | 103401034 | 1 | 20787 | 0 | 0 | 20787 |
| S/G/Y/R/B/O |
NT_009743 | AC021058 | 103401034 | 3 | chr12 | NT_009743 | AC025577 | 103484901 | 3 | 42155 | 0 | 0 | 42155 |
| S/G/Y/R/B/O |
NT_009743 | AC021058 | 103401034 | 3 |   |   | AC026107 | 103484901 | 1 | 104552 | 0 | 0 | 104552 |
| S/G/Y/R/B/O |
NT_009743 | AC025577 | 103484901 | 3 | chr12 | NT_009743 | AC079952 | 103596648 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009743 | AC025577 | 103484901 | 3 |   |   | AC026107 | 103401034 | 1 | 124118 | 0 | 0 | 124118 |
| S/G/Y/R/B/O |
NT_009743 | AC079952 | 103596648 | 1 | chr12 | NT_009743 | AF404777 | 103610194 | 3 | 165873 | 0 | 0 | 165873 |
| S/G/Y/R/B/O |
NT_009743 | AC079952 | 103596648 | 1 | chr12 | NT_033257 | AC069227 | 103882085 | 3 | 165832 | 0 | 0 | 165832 |
| S/G/Y/R/B/O |
NT_009743 | AC079952 | 103596648 | 1 |   |   | AC018743 | 103401034 | 1 | 10045 | 0 | 20646 | 30691 |
| S/G/Y/R/B/O |
NT_009743 | AC079952 | 103596648 | 1 |   |   | AC073157 | 103882085 | 1 | 117178 | 0 | 0 | 117178 |
| S/G/Y/R/B/O |
NT_009743 | AC079952 | 103596648 | 1 |   |   | AC079625 | 103882085 | 1 | 28116 | 0 | 0 | 28116 |
| S/G/Y/R/B/O |
NT_009743 | AF404777 | 103610194 | 3 | chr12 | NT_009743 | AC027087 | 103817533 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009743 | AF404777 | 103610194 | 3 | chr12 | NT_033257 | AC069227 | 103882085 | 3 | 167347 | 0 | 0 | 167347 |
| S/G/Y/R/B/O |
NT_009743 | AF404777 | 103610194 | 3 |   |   | AC018743 | 103610194 | 1 | 15796 | 0 | 15417 | 31213 |
| S/G/Y/R/B/O |
NT_009743 | AF404777 | 103610194 | 3 |   |   | AC073157 | 103882085 | 1 | 46509 | 0 | 0 | 46509 |
| S/G/Y/R/B/O |
NT_009743 | AF404777 | 103610194 | 3 |   |   | AC079625 | 103882085 | 1 | 52286 | 0 | 0 | 52286 |
| S/G/Y/R/B/O |
NT_009743 | AC027087 | 103817533 | 1 |   |   |   |   |   |   |   |   |   |
| S/G/Y/R/B/O |
NT_009743 | AC027087 | 103817533 | 1 | chr12 | NT_009743 | AC023056 | 102383478 | 1 | 39303 | 10722 | 5215 | 55240 |
| S/G/Y/R/B/O |
NT_009743 | AC027087 | 103817533 | 1 | chr12 | NT_009743 | AC026867 | 102629296 | 1 | 17039 | 14985 | 2938 | 34962 |
| S/G/Y/R/B/O |
NT_009743 | AC027087 | 103817533 | 1 | chr12 | NT_009743 | AC063947 | 102437515 | 3 | 45372 | 31227 | 2657 | 79256 |
| S/G/Y/R/B/O |
NT_009743 | AC027087 | 103817533 | 1 | chr12 | NT_009743 | AC063951 | 102256294 | 3 | 25415 | 9014 | 1386 | 35815 |
| S/G/Y/R/B/O |
NT_009743 | AC027087 | 103817533 | 1 |   |   | AC058819 | 102629296 | 1 | 13016 | 2339 | 5901 | 21256 |
| S/G/Y/R/B/O |
NT_009743 | AC027087 | 103817533 | 1 |   |   | AC079953 | 102256294 | 1 | 23914 | 9096 | 6776 | 39786 |
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