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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_009325 | AC104389 | 4682223 | 2 | chr11 | NT_009325 | U01317 | 4736044 | 3 | 26518 | 0 | 0 | 26518 |
| S/G/Y/R/B/O |
NT_009325 | AC104389 | 4682223 | 2 | chr11 | NT_009325 | AC026083 | 5066958 | 1 | 33811 | 0 | 0 | 33811 |
| S/G/Y/R/B/O |
NT_009325 | AC104389 | 4682223 | 2 | chr11 | NT_009325 | AF137396 | 4786048 | 3 | 111334 | 0 | 0 | 111334 |
| S/G/Y/R/B/O |
NT_009325 | AC104389 | 4682223 | 2 |   |   | AC087380 | 5066958 | 3 | 35957 | 0 | 0 | 35957 |
| S/G/Y/R/B/O |
NT_009325 | AC104389 | 4682223 | 2 |   |   | M91036 | 4786048 | 3 | 11330 | 0 | 0 | 11330 |
| S/G/Y/R/B/O |
NT_009325 | AC104389 | 4682223 | 2 |   |   | M91037 | 4786048 | 3 | 11334 | 0 | 0 | 11334 |
| S/G/Y/R/B/O |
NT_009325 | AC104389 | 4682223 | 2 |   |   | NG_000007 | 4786048 | 3 | 80895 | 0 | 0 | 80895 |
| S/G/Y/R/B/O |
NT_009325 | AC104389 | 4682223 | 2 |   |   | V00517 | 4736044 | 3 | 11300 | 0 | 0 | 11300 |
| S/G/Y/R/B/O |
NT_009325 | U01317 | 4736044 | 3 | chr11 | NT_009325 | AF137396 | 4786048 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009325 | U01317 | 4736044 | 3 |   |   | M14292 | 4682223 | 3 | 11125 | 0 | 0 | 11125 |
| S/G/Y/R/B/O |
NT_009325 | U01317 | 4736044 | 3 |   |   | M91036 | 4682223 | 3 | 11345 | 0 | 0 | 11345 |
| S/G/Y/R/B/O |
NT_009325 | U01317 | 4736044 | 3 |   |   | M91037 | 4682223 | 3 | 11291 | 0 | 0 | 11291 |
| S/G/Y/R/B/O |
NT_009325 | U01317 | 4736044 | 3 |   |   | NG_000007 | 4682223 | 3 | 73308 | 0 | 0 | 73308 |
| S/G/Y/R/B/O |
NT_009325 | AF137396 | 4786048 | 3 | chr11 | NT_009325 | AC015691 | 5001138 | 2 | 49520 | 0 | 0 | 49520 |
| S/G/Y/R/B/O |
NT_009325 | AF137396 | 4786048 | 3 | chr11 | NT_009325 | AC011647 | 5015243 | 1 | 18624 | 0 | 0 | 18624 |
| S/G/Y/R/B/O |
NT_009325 | AF137396 | 4786048 | 3 | chr11 | NT_009325 | AC026083 | 5066958 | 1 | 123236 | 2908 | 16224 | 142368 |
| S/G/Y/R/B/O |
NT_009325 | AF137396 | 4786048 | 3 | chr11 | NT_009325 | AC104389 | 4682223 | 2 | 111334 | 0 | 0 | 111334 |
| S/G/Y/R/B/O |
NT_009325 | AF137396 | 4786048 | 3 |   |   | AC087380 | 5066958 | 3 | 157885 | 0 | 0 | 157885 |
| S/G/Y/R/B/O |
NT_009325 | AC015691 | 5001138 | 2 | chr11 | NT_009325 | AC011647 | 5015243 | 1 | 129084 | 0 | 0 | 129084 |
| S/G/Y/R/B/O |
NT_009325 | AC015691 | 5001138 | 2 | chr11 | NT_009325 | AC026083 | 5066958 | 1 | 18127 | 5491 | 42830 | 66448 |
| S/G/Y/R/B/O |
NT_009325 | AC015691 | 5001138 | 2 | chr11 | NT_009325 | AC026090 | 5481271 | 1 | 39875 | 1986 | 6239 | 48100 |
| S/G/Y/R/B/O |
NT_009325 | AC015691 | 5001138 | 2 | chr11 | NT_009325 | AC109341 | 5087194 | 2 | 72289 | 0 | 0 | 72289 |
| S/G/Y/R/B/O |
NT_009325 | AC015691 | 5001138 | 2 |   |   | AC087380 | 5481271 | 3 | 91907 | 0 | 0 | 91907 |
| S/G/Y/R/B/O |
NT_009325 | AC011647 | 5015243 | 1 | chr11 | NT_009325 | AC026083 | 5066958 | 1 | 11102 | 5468 | 9876 | 26446 |
| S/G/Y/R/B/O |
NT_009325 | AC011647 | 5015243 | 1 | chr11 | NT_009325 | AC109341 | 5087194 | 2 | 13499 | 0 | 0 | 13499 |
| S/G/Y/R/B/O |
NT_009325 | AC011647 | 5015243 | 1 | chr11 | NT_009325 | AF137396 | 4786048 | 3 | 18624 | 0 | 0 | 18624 |
| S/G/Y/R/B/O |
NT_009325 | AC011647 | 5015243 | 1 |   |   | AC087380 | 5066958 | 3 | 88613 | 0 | 0 | 88613 |
| S/G/Y/R/B/O |
NT_009325 | AC026083 | 5066958 | 1 | chr11 | NT_009325 | AC109341 | 5087194 | 2 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009325 | AC026083 | 5066958 | 1 | chr11 | NT_009325 | AC015691 | 5001138 | 2 | 18127 | 5491 | 42830 | 66448 |
| S/G/Y/R/B/O |
NT_009325 | AC026083 | 5066958 | 1 | chr11 | NT_009325 | AC104389 | 4682223 | 2 | 33811 | 0 | 0 | 33811 |
| S/G/Y/R/B/O |
NT_009325 | AC026083 | 5066958 | 1 | chr11 | NT_009325 | AF137396 | 4786048 | 3 | 123236 | 2908 | 16224 | 142368 |
| S/G/Y/R/B/O |
NT_009325 | AC026083 | 5066958 | 1 |   |   | AC087380 | 5001138 | 3 | 123571 | 5495 | 54966 | 184032 |
| S/G/Y/R/B/O |
NT_009325 | AC109341 | 5087194 | 2 | chr11 | NT_009325 | AC111177 | 5181302 | 2 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009325 | AC109341 | 5087194 | 2 | chr11 | NT_009325 | AC011647 | 5015243 | 1 | 13499 | 0 | 0 | 13499 |
| S/G/Y/R/B/O |
NT_009325 | AC109341 | 5087194 | 2 | chr11 | NT_009325 | AC015691 | 5001138 | 2 | 72289 | 0 | 0 | 72289 |
| S/G/Y/R/B/O |
NT_009325 | AC109341 | 5087194 | 2 | chr11 | NT_009325 | AC019088 | 5231024 | 1 | 10444 | 5344 | 4099 | 19887 |
| S/G/Y/R/B/O |
NT_009325 | AC109341 | 5087194 | 2 | chr11 | NT_009325 | AC026090 | 5481271 | 1 | 105971 | 1983 | 27143 | 135097 |
| S/G/Y/R/B/O |
NT_009325 | AC111177 | 5181302 | 2 | chr11 | NT_009325 | AC009642 | 5227614 | 1 | 61570 | 12065 | 29544 | 103179 |
| S/G/Y/R/B/O |
NT_009325 | AC111177 | 5181302 | 2 | chr11 | NT_009325 | AC022762 | 5524760 | 2 | 43594 | 0 | 11123 | 54717 |
| S/G/Y/R/B/O |
NT_009325 | AC111177 | 5181302 | 2 |   |   | AC021935 | 5227614 | 1 | 43586 | 0 | 1075 | 44661 |
| S/G/Y/R/B/O |
NT_009325 | AC009642 | 5227614 | 1 | chr11 | NT_009325 | AC019088 | 5231024 | 1 | 14420 | 4578 | 12623 | 31621 |
| S/G/Y/R/B/O |
NT_009325 | AC019088 | 5231024 | 1 | chr11 | NT_009325 | AC026090 | 5481271 | 1 | 0 | 2740 | 1225 | 3965 |
| S/G/Y/R/B/O |
NT_009325 | AC019088 | 5231024 | 1 | chr11 | NT_009325 | AC109341 | 5087194 | 2 | 10444 | 5344 | 4099 | 19887 |
| S/G/Y/R/B/O |
NT_009325 | AC026090 | 5481271 | 1 | chr11 | NT_009325 | AC022762 | 5524760 | 2 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009325 | AC026090 | 5481271 | 1 | chr11 | NT_009325 | AC015691 | 5001138 | 2 | 39875 | 1986 | 6239 | 48100 |
| S/G/Y/R/B/O |
NT_009325 | AC026090 | 5481271 | 1 | chr11 | NT_009325 | AC109341 | 5087194 | 2 | 105971 | 1983 | 27143 | 135097 |
| S/G/Y/R/B/O |
NT_009325 | AC022762 | 5524760 | 2 | chr11 | NT_009325 | AC036216 | 5700236 | 1 | 120988 | 5960 | 2768 | 129716 |
| S/G/Y/R/B/O |
NT_009325 | AC022762 | 5524760 | 2 | chr11 | NT_009325 | AC111177 | 5181302 | 2 | 43594 | 0 | 11123 | 54717 |
| S/G/Y/R/B/O |
NT_009325 | AC022762 | 5524760 | 2 |   |   | AC021935 | 5227614 | 1 | 161419 | 0 | 1075 | 162494 |
| S/G/Y/R/B/O |
NT_009325 | AC036216 | 5700236 | 1 | chr11 | NT_009325 | AC068733 | 5709170 | 2 | 26331 | 4795 | 702 | 31828 |
| S/G/Y/R/B/O |
NT_009325 | AC036216 | 5700236 | 1 |   |   | AC021935 | 5181302 | 1 | 101485 | 3933 | 2767 | 108185 |
| S/G/Y/R/B/O |
NT_009325 | AC068733 | 5709170 | 2 | chr11 | NT_009325 | AC084337 | 5798944 | 2 | 106171 | 0 | 0 | 106171 |
| S/G/Y/R/B/O |
NT_009325 | AC068733 | 5709170 | 2 |   |   | AC024232 | 5524760 | 1 | 73275 | 0 | 57575 | 130850 |
| S/G/Y/R/B/O |
NT_009325 | AC084337 | 5798944 | 2 | chr11 | NT_009325 | AC009796 | 5953369 | 2 | 67228 | 0 | 0 | 67228 |
| S/G/Y/R/B/O |
NT_009325 | AC084337 | 5798944 | 2 |   |   | AC024232 | 5953369 | 1 | 24913 | 0 | 57600 | 82513 |
| S/G/Y/R/B/O |
NT_009325 | AC009796 | 5953369 | 2 | chr11 | NT_009325 | AC091564 | 6078289 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009325 | AC009796 | 5953369 | 2 | chr11 | NT_009325 | AC027641 | 6085814 | 1 | 45653 | 0 | 0 | 45653 |
| S/G/Y/R/B/O |
NT_009325 | AC091564 | 6078289 | 1 | chr11 | NT_009325 | AC027641 | 6085814 | 1 | 0 | 2347 | 111307 | 113654 |
| S/G/Y/R/B/O |
NT_009325 | AC027641 | 6085814 | 1 | chr11 | NT_009325 | AC087280 | 6265290 | 3 | 36229 | 0 | 4756 | 40985 |
| S/G/Y/R/B/O |
NT_009325 | AC027641 | 6085814 | 1 | chr11 | NT_009325 | AC009796 | 5953369 | 2 | 45653 | 0 | 0 | 45653 |
| S/G/Y/R/B/O |
NT_009325 | AC027641 | 6085814 | 1 |   |   | AF321237 | 6078289 | 3 | 18990 | 0 | 4815 | 23805 |
| S/G/Y/R/B/O |
NT_009325 | AC087280 | 6265290 | 3 | chr11 | NT_009325 | AC090160 | 6429207 | 2 | 30192 | 0 | 0 | 30192 |
| S/G/Y/R/B/O |
NT_009325 | AC087280 | 6265290 | 3 |   |   | AC017103 | 6078289 | 1 | 140346 | 1723 | 6742 | 148811 |
| S/G/Y/R/B/O |
NT_009325 | AC087280 | 6265290 | 3 |   |   | AC024729 | 6078289 | 1 | 27678 | 2454 | 0 | 30132 |
| S/G/Y/R/B/O |
NT_009325 | AC087280 | 6265290 | 3 |   |   | AF321237 | 6078289 | 3 | 110352 | 0 | 0 | 110352 |
| S/G/Y/R/B/O |
NT_009325 | AC087280 | 6265290 | 3 |   |   | Z68344 | 6078289 | 3 | 12852 | 0 | 0 | 12852 |
| S/G/Y/R/B/O |
NT_009325 | AC090160 | 6429207 | 2 | chr11 | NT_009325 | AC100875 | 6569116 | 2 | 119613 | 0 | 0 | 119613 |
| S/G/Y/R/B/O |
NT_009325 | AC090160 | 6429207 | 2 |   |   | AC017103 | 6078289 | 1 | 27040 | 0 | 0 | 27040 |
| S/G/Y/R/B/O |
NT_009325 | AC090160 | 6429207 | 2 |   |   | AC024729 | 6078289 | 1 | 124517 | 14813 | 16059 | 155389 |
| S/G/Y/R/B/O |
NT_009325 | AC090160 | 6429207 | 2 |   |   | Z68344 | 6569116 | 3 | 34464 | 0 | 0 | 34464 |
| S/G/Y/R/B/O |
NT_009325 | AC090160 | 6429207 | 2 |   |   | Z68746 | 6569116 | 3 | 37602 | 0 | 0 | 37602 |
| S/G/Y/R/B/O |
NT_009325 | AC100875 | 6569116 | 2 | chr11 | NT_009325 | AC027804 | 6601763 | 2 | 42599 | 0 | 0 | 42599 |
| S/G/Y/R/B/O |
NT_009325 | AC100875 | 6569116 | 2 |   |   | AC024729 | 6569116 | 1 | 71629 | 12156 | 15983 | 99768 |
| S/G/Y/R/B/O |
NT_009325 | AC027804 | 6601763 | 2 | chr11 | NT_009325 | AC060799 | 6774035 | 3 | 15778 | 0 | 0 | 15778 |
| S/G/Y/R/B/O |
NT_009325 | AC027804 | 6601763 | 2 | chr11 | NT_009325 | AC024048 | 6943895 | 1 | 45422 | 1735 | 17512 | 64669 |
| S/G/Y/R/B/O |
NT_009325 | AC060799 | 6774035 | 3 | chr11 | NT_009325 | AC107884 | 6910421 | 2 | 12920 | 0 | 0 | 12920 |
| S/G/Y/R/B/O |
NT_009325 | AC060799 | 6774035 | 3 | chr11 | NT_009325 | AC024048 | 6943895 | 1 | 82848 | 17327 | 2736 | 102911 |
| S/G/Y/R/B/O |
NT_009325 | AC107884 | 6910421 | 2 | chr11 | NT_009325 | AC024048 | 6943895 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009325 | AC107884 | 6910421 | 2 | chr11 | NT_009325 | AC012228 | 7020869 | 2 | 52468 | 0 | 0 | 52468 |
| S/G/Y/R/B/O |
NT_009325 | AC024048 | 6943895 | 1 | chr11 | NT_009325 | AC012228 | 7020869 | 2 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_009325 | AC024048 | 6943895 | 1 | chr11 | NT_009325 | AC027804 | 6601763 | 2 | 45422 | 1735 | 17512 | 64669 |
| S/G/Y/R/B/O |
NT_009325 | AC024048 | 6943895 | 1 | chr11 | NT_009325 | AC060799 | 6774035 | 3 | 82848 | 17327 | 2736 | 102911 |
| S/G/Y/R/B/O |
NT_009325 | AC012228 | 7020869 | 2 |   |   |   |   |   |   |   |   |   |
| S/G/Y/R/B/O |
NT_009325 | AC012228 | 7020869 | 2 | chr11 | NT_009325 | AC107884 | 6910421 | 2 | 52468 | 0 | 0 | 52468 |
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