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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_009563 | AC021103 | 54207661 | 1 | chr12 | NT_009563 | AC073611 | 54211367 | 1 | 81745 | 9736 | 19644 | 111125 |
| S/G/Y/R/B/O |
NT_009563 | AC021103 | 54207661 | 1 | chr12 | NT_009563 | AC068889 | 54338727 | 1 | 28835 | 4283 | 21078 | 54196 |
| S/G/Y/R/B/O |
NT_009563 | AC073611 | 54211367 | 1 | chr12 | NT_009563 | AC068986 | 54211803 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009563 | AC073611 | 54211367 | 1 |   |   | AJ297977 | 54338727 | 3 | 14091 | 0 | 0 | 14091 |
| S/G/Y/R/B/O |
NT_009563 | AC068986 | 54211803 | 1 | chr12 | NT_009563 | AC073594 | 54228786 | 1 | 60817 | 0 | 38534 | 99351 |
| S/G/Y/R/B/O |
NT_009563 | AC068986 | 54211803 | 1 | chr12 | NT_009563 | AC010892 | 54236713 | 1 | 21399 | 0 | 23895 | 45294 |
| S/G/Y/R/B/O |
NT_009563 | AC068986 | 54211803 | 1 | chr12 | NT_009563 | AC023509 | 54313949 | 1 | 63993 | 0 | 0 | 63993 |
| S/G/Y/R/B/O |
NT_009563 | AC068986 | 54211803 | 1 | chr12 | NT_009563 | AC076968 | 54429289 | 3 | 25426 | 0 | 0 | 25426 |
| S/G/Y/R/B/O |
NT_009563 | AC068986 | 54211803 | 1 |   |   | X69908 | 54429289 | 3 | 15008 | 0 | 0 | 15008 |
| S/G/Y/R/B/O |
NT_009563 | AC073594 | 54228786 | 1 | chr12 | NT_009563 | AC012144 | 54231280 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009563 | AC073594 | 54228786 | 1 | chr12 | NT_009563 | AC010892 | 54236713 | 1 | 56170 | 0 | 41178 | 97348 |
| S/G/Y/R/B/O |
NT_009563 | AC073594 | 54228786 | 1 | chr12 | NT_009563 | AC076968 | 54429289 | 3 | 75782 | 0 | 18882 | 94664 |
| S/G/Y/R/B/O |
NT_009563 | AC073594 | 54228786 | 1 |   |   | AC016458 | 54236713 | 1 | 43191 | 2138 | 0 | 45329 |
| S/G/Y/R/B/O |
NT_009563 | AC073594 | 54228786 | 1 |   |   | X69908 | 54429289 | 3 | 12080 | 0 | 3386 | 15466 |
| S/G/Y/R/B/O |
NT_009563 | AC012144 | 54231280 | 1 | chr12 | NT_009563 | AC010892 | 54236713 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009563 | AC012144 | 54231280 | 1 | chr13 | NT_009952 | AL358855 | 103638504 | 3 | 124006 | 3186 | 1817 | 129009 |
| S/G/Y/R/B/O |
NT_009563 | AC012144 | 54231280 | 1 | chr13 | NT_009952 | AL445226 | 103582365 | 3 | 30673 | 2863 | 11725 | 45261 |
| S/G/Y/R/B/O |
NT_009563 | AC012144 | 54231280 | 1 |   |   | AC055118 | 54763469 | 1 | 59630 | 2310 | 1816 | 63756 |
| S/G/Y/R/B/O |
NT_009563 | AC010892 | 54236713 | 1 | chr12 | NT_009563 | AC023509 | 54313949 | 1 | 0 | 0 | 4616 | 4616 |
| S/G/Y/R/B/O |
NT_009563 | AC010892 | 54236713 | 1 | chr12 | NT_009563 | AC068986 | 54211803 | 1 | 21399 | 0 | 23895 | 45294 |
| S/G/Y/R/B/O |
NT_009563 | AC010892 | 54236713 | 1 | chr12 | NT_009563 | AC073594 | 54228786 | 1 | 56170 | 0 | 41178 | 97348 |
| S/G/Y/R/B/O |
NT_009563 | AC010892 | 54236713 | 1 | chr12 | NT_009563 | AC076968 | 54429289 | 3 | 11023 | 0 | 0 | 11023 |
| S/G/Y/R/B/O |
NT_009563 | AC010892 | 54236713 | 1 |   |   | AC016458 | 103582365 | 1 | 14958 | 0 | 0 | 14958 |
| S/G/Y/R/B/O |
NT_009563 | AC023509 | 54313949 | 1 | chr12 | NT_009563 | AC068889 | 54338727 | 1 | 11466 | 0 | 91206 | 102672 |
| S/G/Y/R/B/O |
NT_009563 | AC023509 | 54313949 | 1 | chr12 | NT_009563 | AC068986 | 54211803 | 1 | 63993 | 0 | 0 | 63993 |
| S/G/Y/R/B/O |
NT_009563 | AC068889 | 54338727 | 1 | chr12 | NT_009563 | AC076968 | 54429289 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009563 | AC068889 | 54338727 | 1 | chr12 | NT_009563 | AC021103 | 54207661 | 1 | 28835 | 4283 | 21078 | 54196 |
| S/G/Y/R/B/O |
NT_009563 | AC076968 | 54429289 | 3 | chr12 | NT_009563 | AC012531 | 54632327 | 3 | 40612 | 0 | 0 | 40612 |
| S/G/Y/R/B/O |
NT_009563 | AC076968 | 54429289 | 3 | chr12 | NT_009563 | AC010892 | 54236713 | 1 | 11023 | 0 | 0 | 11023 |
| S/G/Y/R/B/O |
NT_009563 | AC076968 | 54429289 | 3 | chr12 | NT_009563 | AC068986 | 54211803 | 1 | 25426 | 0 | 0 | 25426 |
| S/G/Y/R/B/O |
NT_009563 | AC076968 | 54429289 | 3 | chr12 | NT_009563 | AC073594 | 54228786 | 1 | 75782 | 0 | 18882 | 94664 |
| S/G/Y/R/B/O |
NT_009563 | AC076968 | 54429289 | 3 |   |   | AC016458 | 54632327 | 1 | 147947 | 6387 | 0 | 154334 |
| S/G/Y/R/B/O |
NT_009563 | AC012531 | 54632327 | 3 | chr12 | NT_009563 | AC023794 | 54763469 | 1 | 9154 | 0 | 0 | 9154 |
| S/G/Y/R/B/O |
NT_009563 | AC012531 | 54632327 | 3 |   |   | AC016458 | 54231280 | 1 | 23409 | 2608 | 0 | 26017 |
| S/G/Y/R/B/O |
NT_009563 | AC023794 | 54763469 | 1 | chr12 | NT_009563 | AC025507 | 54969813 | 1 | 97450 | 8711 | 16644 | 122805 |
| S/G/Y/R/B/O |
NT_009563 | AC025507 | 54969813 | 1 | chr12 | NT_009563 | AC078778 | 55014726 | 1 | 19266 | 0 | 0 | 19266 |
| S/G/Y/R/B/O |
NT_009563 | AC078778 | 55014726 | 1 | chr12 | NT_009563 | AC019223 | 55138751 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009563 | AC078778 | 55014726 | 1 | chr12 | NT_009563 | AC079313 | 55514095 | 3 | 69060 | 0 | 0 | 69060 |
| S/G/Y/R/B/O |
NT_009563 | AC019223 | 55138751 | 1 | chr12 | NT_009563 | AC079313 | 55514095 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009563 | AC019223 | 55138751 | 1 | chr12 | NT_009563 | AC024091 | 55965604 | 1 | 59348 | 0 | 0 | 59348 |
| S/G/Y/R/B/O |
NT_009563 | AC019223 | 55138751 | 1 | chr12 | NT_009563 | AC079310 | 55708477 | 3 | 19735 | 0 | 0 | 19735 |
| S/G/Y/R/B/O |
NT_009563 | AC019223 | 55138751 | 1 | chr12 | NT_009563 | AC079842 | 55988193 | 3 | 51232 | 0 | 1498 | 52730 |
| S/G/Y/R/B/O |
NT_009563 | AC019223 | 55138751 | 1 | chr12 | NT_009563 | AC107617 | 55889252 | 1 | 18909 | 0 | 0 | 18909 |
| S/G/Y/R/B/O |
NT_009563 | AC019223 | 55138751 | 1 |   |   | AC025686 | 55965604 | 1 | 24236 | 6409 | 1132 | 31777 |
| S/G/Y/R/B/O |
NT_009563 | AC079313 | 55514095 | 3 | chr12 | NT_009563 | AC025570 | 55674327 | 3 | 62039 | 0 | 0 | 62039 |
| S/G/Y/R/B/O |
NT_009563 | AC079313 | 55514095 | 3 | chr12 | NT_009563 | AC078778 | 55014726 | 1 | 69060 | 0 | 0 | 69060 |
| S/G/Y/R/B/O |
NT_009563 | AC079313 | 55514095 | 3 |   |   | AC053540 | 55674327 | 1 | 58046 | 6238 | 36982 | 101266 |
| S/G/Y/R/B/O |
NT_009563 | AC025570 | 55674327 | 3 | chr12 | NT_009563 | AC068789 | 55676329 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009563 | AC025570 | 55674327 | 3 |   |   | AC053540 | 55014726 | 1 | 41508 | 2070 | 11438 | 55016 |
| S/G/Y/R/B/O |
NT_009563 | AC068789 | 55676329 | 3 | chr12 | NT_009563 | AC079310 | 55708477 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009563 | AC068789 | 55676329 | 3 |   |   | AC053540 | 55514095 | 1 | 21634 | 1328 | 10341 | 33303 |
| S/G/Y/R/B/O |
NT_009563 | AC079310 | 55708477 | 3 | chr12 | NT_009563 | AC107617 | 55889252 | 1 | 68932 | 0 | 21147 | 90079 |
| S/G/Y/R/B/O |
NT_009563 | AC079310 | 55708477 | 3 | chr12 | NT_009563 | AC019223 | 55138751 | 1 | 19735 | 0 | 0 | 19735 |
| S/G/Y/R/B/O |
NT_009563 | AC079310 | 55708477 | 3 |   |   | AC025686 | 55138751 | 1 | 92469 | 7529 | 12025 | 112023 |
| S/G/Y/R/B/O |
NT_009563 | AC079310 | 55708477 | 3 |   |   | AC053540 | 55138751 | 1 | 17884 | 4214 | 20706 | 42804 |
| S/G/Y/R/B/O |
NT_009563 | AC079310 | 55708477 | 3 |   |   | AY005150 | 55889252 | 3 | 12351 | 0 | 0 | 12351 |
| S/G/Y/R/B/O |
NT_009563 | AC107617 | 55889252 | 1 | chr12 | NT_009563 | AC024091 | 55965604 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009563 | AC107617 | 55889252 | 1 | chr12 | NT_009563 | AC019223 | 55138751 | 1 | 18909 | 0 | 0 | 18909 |
| S/G/Y/R/B/O |
NT_009563 | AC107617 | 55889252 | 1 |   |   | AC025686 | 55138751 | 1 | 82280 | 7549 | 21712 | 111541 |
| S/G/Y/R/B/O |
NT_009563 | AC107617 | 55889252 | 1 |   |   | AY005150 | 55708477 | 3 | 12352 | 0 | 0 | 12352 |
| S/G/Y/R/B/O |
NT_009563 | AC024091 | 55965604 | 1 | chr12 | NT_009563 | AC079842 | 55988193 | 3 | 122080 | 0 | 0 | 122080 |
| S/G/Y/R/B/O |
NT_009563 | AC024091 | 55965604 | 1 | chr12 | NT_009563 | AC019223 | 55138751 | 1 | 59348 | 0 | 0 | 59348 |
| S/G/Y/R/B/O |
NT_009563 | AC024091 | 55965604 | 1 | chr12 | NT_009563 | AC027287 | 56121193 | 3 | 61010 | 0 | 0 | 61010 |
| S/G/Y/R/B/O |
NT_009563 | AC079842 | 55988193 | 3 | chr12 | NT_009563 | AC027287 | 56121193 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009563 | AC079842 | 55988193 | 3 | chr12 | NT_009563 | AC019223 | 55138751 | 1 | 51232 | 0 | 1498 | 52730 |
| S/G/Y/R/B/O |
NT_009563 | AC027287 | 56121193 | 3 | chr12 | NT_009563 | AC090048 | 56319238 | 1 | 137457 | 0 | 0 | 137457 |
| S/G/Y/R/B/O |
NT_009563 | AC027287 | 56121193 | 3 | chr12 | NT_009563 | AC024091 | 55965604 | 1 | 61010 | 0 | 0 | 61010 |
| S/G/Y/R/B/O |
NT_009563 | AC027287 | 56121193 | 3 |   |   | AC022207 | 55965604 | 1 | 113218 | 0 | 19047 | 132265 |
| S/G/Y/R/B/O |
NT_009563 | AC090048 | 56319238 | 1 |   |   |   |   |   |   |   |   |   |
| S/G/Y/R/B/O |
NT_009563 | AC090048 | 56319238 | 1 |   |   | AC022207 | 56319238 | 1 | 163509 | 0 | 16513 | 180022 |
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