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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_006547 | AC090075 | 24851257 | 1 | chr5 | NT_006547 | AC012059 | 24878744 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_006547 | AC090075 | 24851257 | 1 | chr5 | NT_006547 | AC010347 | 26202159 | 3 | 24042 | 0 | 15851 | 39893 |
| S/G/Y/R/B/O |
NT_006547 | AC090075 | 24851257 | 1 | chr3 | NT_022517 | AC104183 | 19964313 | 1 | 31594 | 2381 | 15783 | 49758 |
| S/G/Y/R/B/O |
NT_006547 | AC090075 | 24851257 | 1 | chr3 | NT_022517 | AC104441 | 19799444 | 1 | 31563 | 0 | 45530 | 77093 |
| S/G/Y/R/B/O |
NT_006547 | AC090075 | 24851257 | 1 |   |   | AC094093 | 26109026 | 1 | 21381 | 0 | 13039 | 34420 |
| S/G/Y/R/B/O |
NT_006547 | AC012059 | 24878744 | 1 | chr5 | NT_006547 | AC010387 | 24948738 | 3 | 117094 | 2415 | 0 | 119509 |
| S/G/Y/R/B/O |
NT_006547 | AC010387 | 24948738 | 3 | chr5 | NT_006547 | AC091885 | 25122152 | 3 | 13254 | 0 | 0 | 13254 |
| S/G/Y/R/B/O |
NT_006547 | AC010387 | 24948738 | 3 |   |   | AC027469 | 24878744 | 1 | 13254 | 0 | 0 | 13254 |
| S/G/Y/R/B/O |
NT_006547 | AC091885 | 25122152 | 3 | chr5 | NT_006547 | AC109483 | 25276182 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_006547 | AC091885 | 25122152 | 3 |   |   | AC010775 | 24948738 | 1 | 13062 | 0 | 0 | 13062 |
| S/G/Y/R/B/O |
NT_006547 | AC091885 | 25122152 | 3 |   |   | AC027469 | 24948738 | 1 | 133384 | 2833 | 25377 | 161594 |
| S/G/Y/R/B/O |
NT_006547 | AC109483 | 25276182 | 3 | chr5 | NT_006547 | AC091893 | 25337958 | 3 | 33391 | 0 | 0 | 33391 |
| S/G/Y/R/B/O |
NT_006547 | AC109483 | 25276182 | 3 |   |   | AC010775 | 24948738 | 1 | 48600 | 0 | 5418 | 54018 |
| S/G/Y/R/B/O |
NT_006547 | AC091893 | 25337958 | 3 | chr5 | NT_006547 | AC106821 | 25458931 | 3 | 36072 | 0 | 0 | 36072 |
| S/G/Y/R/B/O |
NT_006547 | AC091893 | 25337958 | 3 |   |   | AC010775 | 25337958 | 1 | 109319 | 5351 | 8438 | 123108 |
| S/G/Y/R/B/O |
NT_006547 | AC091893 | 25337958 | 3 |   |   | AC025113 | 25337958 | 1 | 20066 | 0 | 11598 | 31664 |
| S/G/Y/R/B/O |
NT_006547 | AC106821 | 25458931 | 3 | chr5 | NT_006547 | AC026428 | 25574126 | 3 | 47511 | 0 | 0 | 47511 |
| S/G/Y/R/B/O |
NT_006547 | AC106821 | 25458931 | 3 |   |   | AC010775 | 15951414 | 1 | 11744 | 0 | 0 | 11744 |
| S/G/Y/R/B/O |
NT_006547 | AC106821 | 25458931 | 3 |   |   | AC025113 | 15951414 | 1 | 102114 | 7758 | 6155 | 116027 |
| S/G/Y/R/B/O |
NT_006547 | AC026428 | 25574126 | 3 | chr5 | NT_006547 | AC025189 | 25611724 | 3 | 37549 | 0 | 0 | 37549 |
| S/G/Y/R/B/O |
NT_006547 | AC026428 | 25574126 | 3 |   |   | AC025113 | 15951414 | 1 | 36807 | 4892 | 4662 | 46361 |
| S/G/Y/R/B/O |
NT_006547 | AC025189 | 25611724 | 3 | chr5 | NT_006547 | AC106810 | 25730998 | 3 | 29807 | 0 | 0 | 29807 |
| S/G/Y/R/B/O |
NT_006547 | AC025189 | 25611724 | 3 |   |   | AC025676 | 25458931 | 1 | 79621 | 0 | 1268 | 80889 |
| S/G/Y/R/B/O |
NT_006547 | AC106810 | 25730998 | 3 | chr5 | NT_006547 | AC099499 | 25793038 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_006547 | AC106810 | 25730998 | 3 | chr5 | NT_006547 | AC023980 | 25938053 | 1 | 12123 | 5364 | 0 | 17487 |
| S/G/Y/R/B/O |
NT_006547 | AC106810 | 25730998 | 3 |   |   | AC025676 | 25611724 | 1 | 66399 | 0 | 3017 | 69416 |
| S/G/Y/R/B/O |
NT_006547 | AC099499 | 25793038 | 3 | chr5 | NT_006547 | AC106754 | 25920524 | 2 | 27041 | 0 | 0 | 27041 |
| S/G/Y/R/B/O |
NT_006547 | AC099499 | 25793038 | 3 | chr5 | NT_006547 | AC023980 | 25938053 | 1 | 111231 | 11483 | 14048 | 136762 |
| S/G/Y/R/B/O |
NT_006547 | AC099499 | 25793038 | 3 | chr5 | NT_006547 | AC032041 | 25937723 | 1 | 80850 | 7183 | 0 | 88033 |
| S/G/Y/R/B/O |
NT_006547 | AC099499 | 25793038 | 3 |   |   | AC025676 | 25938053 | 1 | 19498 | 0 | 0 | 19498 |
| S/G/Y/R/B/O |
NT_006547 | AC106754 | 25920524 | 2 | chr5 | NT_006547 | AC032041 | 25937723 | 1 | 106293 | 8668 | 1115 | 116076 |
| S/G/Y/R/B/O |
NT_006547 | AC106754 | 25920524 | 2 | chr5 | NT_006547 | AC022140 | 26109026 | 3 | 46855 | 0 | 0 | 46855 |
| S/G/Y/R/B/O |
NT_006547 | AC106754 | 25920524 | 2 | chr5 | NT_006547 | AC023980 | 25938053 | 1 | 15759 | 0 | 0 | 15759 |
| S/G/Y/R/B/O |
NT_006547 | AC032041 | 25937723 | 1 | chr5 | NT_006547 | AC023980 | 25938053 | 1 | 31652 | 5388 | 0 | 37040 |
| S/G/Y/R/B/O |
NT_006547 | AC032041 | 25937723 | 1 | chr5 | NT_006547 | AC099499 | 25793038 | 3 | 80850 | 7183 | 0 | 88033 |
| S/G/Y/R/B/O |
NT_006547 | AC023980 | 25938053 | 1 | chr5 | NT_006547 | AC022140 | 26109026 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_006547 | AC023980 | 25938053 | 1 | chr5 | NT_006547 | AC099499 | 25793038 | 3 | 111231 | 11483 | 14048 | 136762 |
| S/G/Y/R/B/O |
NT_006547 | AC023980 | 25938053 | 1 | chr5 | NT_006547 | AC106754 | 25920524 | 2 | 15759 | 0 | 0 | 15759 |
| S/G/Y/R/B/O |
NT_006547 | AC023980 | 25938053 | 1 | chr5 | NT_006547 | AC106810 | 25730998 | 3 | 12123 | 5364 | 0 | 17487 |
| S/G/Y/R/B/O |
NT_006547 | AC023980 | 25938053 | 1 |   |   | AC025676 | 25920524 | 1 | 12118 | 5362 | 1219 | 18699 |
| S/G/Y/R/B/O |
NT_006547 | AC022140 | 26109026 | 3 | chr5 | NT_006547 | AC010347 | 26202159 | 3 | 20057 | 0 | 0 | 20057 |
| S/G/Y/R/B/O |
NT_006547 | AC022140 | 26109026 | 3 | chr5 | NT_006547 | AC106754 | 25920524 | 2 | 46855 | 0 | 0 | 46855 |
| S/G/Y/R/B/O |
NT_006547 | AC022140 | 26109026 | 3 |   |   | AC094093 | 24851257 | 1 | 16525 | 0 | 4365 | 20890 |
| S/G/Y/R/B/O |
NT_006547 | AC010347 | 26202159 | 3 | chr5 | NT_006547 | AC022418 | 26328740 | 3 | 28438 | 0 | 0 | 28438 |
| S/G/Y/R/B/O |
NT_006547 | AC010347 | 26202159 | 3 | chr5 | NT_006547 | AC090075 | 24851257 | 1 | 24042 | 0 | 15851 | 39893 |
| S/G/Y/R/B/O |
NT_006547 | AC010347 | 26202159 | 3 |   |   | AC094093 | 24851257 | 1 | 42658 | 0 | 22135 | 64793 |
| S/G/Y/R/B/O |
NT_006547 | AC022418 | 26328740 | 3 | chr5 | NT_006547 | AC022448 | 26445376 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_006547 | AC022418 | 26328740 | 3 | chr5 | NT_006547 | AC093212 | 26654075 | 1 | 57775 | 0 | 0 | 57775 |
| S/G/Y/R/B/O |
NT_006547 | AC022418 | 26328740 | 3 |   |   | AC012631 | 26202159 | 2 | 33011 | 0 | 13273 | 46284 |
| S/G/Y/R/B/O |
NT_006547 | AC022448 | 26445376 | 3 | chr5 | NT_006547 | AC010498 | 26583601 | 3 | 83745 | 0 | 0 | 83745 |
| S/G/Y/R/B/O |
NT_006547 | AC022448 | 26445376 | 3 | chr5 | NT_006547 | AC010474 | 26598420 | 3 | 34122 | 0 | 0 | 34122 |
| S/G/Y/R/B/O |
NT_006547 | AC022448 | 26445376 | 3 | chr5 | NT_006547 | AC093212 | 26654075 | 1 | 107092 | 0 | 0 | 107092 |
| S/G/Y/R/B/O |
NT_006547 | AC022448 | 26445376 | 3 |   |   | AC012631 | 26583601 | 2 | 31541 | 0 | 8209 | 39750 |
| S/G/Y/R/B/O |
NT_006547 | AC010498 | 26583601 | 3 | chr5 | NT_006547 | AC010474 | 26598420 | 3 | 47213 | 0 | 0 | 47213 |
| S/G/Y/R/B/O |
NT_006547 | AC010498 | 26583601 | 3 | chr5 | NT_006547 | AC093212 | 26654075 | 1 | 29166 | 0 | 0 | 29166 |
| S/G/Y/R/B/O |
NT_006547 | AC010474 | 26598420 | 3 | chr5 | NT_006547 | AC109469 | 26639265 | 1 | 9582 | 0 | 73963 | 83545 |
| S/G/Y/R/B/O |
NT_006547 | AC010474 | 26598420 | 3 | chr5 | NT_006547 | AC022448 | 26445376 | 3 | 34122 | 0 | 0 | 34122 |
| S/G/Y/R/B/O |
NT_006547 | AC010474 | 26598420 | 3 | chr5 | NT_023162 | AC113370 | 26996621 | 1 | 33718 | 0 | 0 | 33718 |
| S/G/Y/R/B/O |
NT_006547 | AC109469 | 26639265 | 1 | chr5 | NT_006547 | AC093212 | 26654075 | 1 | 3809 | 0 | 0 | 3809 |
| S/G/Y/R/B/O |
NT_006547 | AC109469 | 26639265 | 1 | chr5 | NT_023162 | AC113370 | 26996621 | 1 | 49170 | 0 | 51074 | 100244 |
| S/G/Y/R/B/O |
NT_006547 | AC093212 | 26654075 | 1 |   |   |   |   |   |   |   |   |   |
| S/G/Y/R/B/O |
NT_006547 | AC093212 | 26654075 | 1 | chr5 | NT_006547 | AC010498 | 26583601 | 3 | 29166 | 0 | 0 | 29166 |
| S/G/Y/R/B/O |
NT_006547 | AC093212 | 26654075 | 1 | chr5 | NT_006547 | AC022418 | 26328740 | 3 | 57775 | 0 | 0 | 57775 |
| S/G/Y/R/B/O |
NT_006547 | AC093212 | 26654075 | 1 | chr5 | NT_006547 | AC022448 | 26445376 | 3 | 107092 | 0 | 0 | 107092 |
| S/G/Y/R/B/O |
NT_006547 | AC093212 | 26654075 | 1 |   |   | AC012631 | 50555447 | 2 | 43856 | 1511 | 8221 | 53588 |
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