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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_011754 | AL355923 | 15197484 | 2 | chrX | NT_011754 | AC025239 | 15197919 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011754 | AC025239 | 15197919 | 1 | chrX | NT_011754 | AC023037 | 15203342 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011754 | AC025239 | 15197919 | 1 | chrX | NT_011754 | AC003667 | 18074491 | 3 | 61732 | 4072 | 3186 | 68990 |
| S/G/Y/R/B/O |
NT_011754 | AC025239 | 15197919 | 1 | chrX | NT_011754 | AC112916 | 18206506 | 3 | 41350 | 2954 | 36845 | 81149 |
| S/G/Y/R/B/O |
NT_011754 | AC025239 | 15197919 | 1 |   |   | AC097348 | 18074491 | 3 | 41350 | 2953 | 36845 | 81148 |
| S/G/Y/R/B/O |
NT_011754 | AC023037 | 15203342 | 1 | chrX | NT_011754 | AC073617 | 15221229 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011754 | AC023037 | 15203342 | 1 | chrX | NT_011754 | AC003659 | 18042305 | 1 | 10575 | 23094 | 36231 | 69900 |
| S/G/Y/R/B/O |
NT_011754 | AC073617 | 15221229 | 3 | chrX | NT_011754 | AC074035 | 15370531 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011754 | AC074035 | 15370531 | 3 | chrX | NT_011754 | AC108683 | 15527241 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011754 | AC108683 | 15527241 | 3 | chrX | NT_011754 | AC079264 | 15586615 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011754 | AC108683 | 15527241 | 3 |   |   | AC055112 | 15197484 | 1 | 25300 | 0 | 0 | 25300 |
| S/G/Y/R/B/O |
NT_011754 | AC108683 | 15527241 | 3 |   |   | AC073615 | 15197484 | 1 | 13522 | 4831 | 2467 | 20820 |
| S/G/Y/R/B/O |
NT_011754 | AC108683 | 15527241 | 3 |   |   | AC116545 | 16962465 | 3 | 25298 | 0 | 0 | 25298 |
| S/G/Y/R/B/O |
NT_011754 | AC079264 | 15586615 | 3 | chrX | NT_011754 | AC112917 | 15779475 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011754 | AC079264 | 15586615 | 3 | chr12 | NT_009743 | AC073833 | 101429327 | 1 | 19824 | 10034 | 24890 | 54748 |
| S/G/Y/R/B/O |
NT_011754 | AC079264 | 15586615 | 3 |   |   | AC015503 | 67135055 | 1 | 110459 | 4283 | 0 | 114742 |
| S/G/Y/R/B/O |
NT_011754 | AC079264 | 15586615 | 3 |   |   | AC015648 | 67135055 | 1 | 22288 | 1699 | 0 | 23987 |
| S/G/Y/R/B/O |
NT_011754 | AC079264 | 15586615 | 3 |   |   | AC055112 | 67135055 | 1 | 86692 | 0 | 1317 | 88009 |
| S/G/Y/R/B/O |
NT_011754 | AC079264 | 15586615 | 3 |   |   | AC073494 | 67135055 | 1 | 53011 | 0 | 18046 | 71057 |
| S/G/Y/R/B/O |
NT_011754 | AC079264 | 15586615 | 3 |   |   | AC073615 | 67135055 | 1 | 47246 | 2530 | 15802 | 65578 |
| S/G/Y/R/B/O |
NT_011754 | AC112917 | 15779475 | 3 | chrX | NT_011754 | AC005297 | 15913664 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011754 | AC112917 | 15779475 | 3 |   |   | AC015648 | 67135055 | 1 | 120281 | 2392 | 1410 | 124083 |
| S/G/Y/R/B/O |
NT_011754 | AC112917 | 15779475 | 3 |   |   | AC073494 | 67135055 | 1 | 68775 | 2063 | 0 | 70838 |
| S/G/Y/R/B/O |
NT_011754 | AC005297 | 15913664 | 3 | chrX | NT_011754 | AC073614 | 16091167 | 3 | 2056 | 0 | 0 | 2056 |
| S/G/Y/R/B/O |
NT_011754 | AC073614 | 16091167 | 3 | chrX | NT_011754 | AC079178 | 16218911 | 3 | 2070 | 0 | 0 | 2070 |
| S/G/Y/R/B/O |
NT_011754 | AC079178 | 16218911 | 3 | chrX | NT_011754 | AC005345 | 16331506 | 3 | 0 | 0 | 243 | 243 |
| S/G/Y/R/B/O |
NT_011754 | AC005345 | 16331506 | 3 | chrX | NT_011754 | AC107293 | 16491702 | 3 | 2040 | 0 | 0 | 2040 |
| S/G/Y/R/B/O |
NT_011754 | AC107293 | 16491702 | 3 | chrX | NT_011754 | AC022356 | 16646011 | 1 | 20203 | 0 | 234 | 20437 |
| S/G/Y/R/B/O |
NT_011754 | AC022356 | 16646011 | 1 | chrX | NT_011754 | AC012687 | 16720154 | 1 | 36022 | 1868 | 1242 | 39132 |
| S/G/Y/R/B/O |
NT_011754 | AC022356 | 16646011 | 1 | chrX | NT_011754 | AC112493 | 16720942 | 3 | 69337 | 2159 | 1242 | 72738 |
| S/G/Y/R/B/O |
NT_011754 | AC012687 | 16720154 | 1 | chrX | NT_011754 | AC112493 | 16720942 | 3 | 111099 | 0 | 29995 | 141094 |
| S/G/Y/R/B/O |
NT_011754 | AC012687 | 16720154 | 1 | chrX | NT_011754 | AC017025 | 16852725 | 1 | 11338 | 0 | 15943 | 27281 |
| S/G/Y/R/B/O |
NT_011754 | AC012687 | 16720154 | 1 | chrX | NT_011754 | AC097262 | 16849365 | 1 | 19373 | 0 | 3160 | 22533 |
| S/G/Y/R/B/O |
NT_011754 | AC112493 | 16720942 | 3 | chrX | NT_011754 | AC097262 | 16849365 | 1 | 19386 | 0 | 0 | 19386 |
| S/G/Y/R/B/O |
NT_011754 | AC112493 | 16720942 | 3 | chrX | NT_011754 | AC017025 | 16852725 | 1 | 31258 | 2183 | 0 | 33441 |
| S/G/Y/R/B/O |
NT_011754 | AC112493 | 16720942 | 3 | chrX | NT_011754 | AC022356 | 16646011 | 1 | 69337 | 2159 | 1242 | 72738 |
| S/G/Y/R/B/O |
NT_011754 | AC097262 | 16849365 | 1 | chrX | NT_011754 | AC017025 | 16852725 | 1 | 79218 | 0 | 20965 | 100183 |
| S/G/Y/R/B/O |
NT_011754 | AC097262 | 16849365 | 1 | chrX | NT_011754 | AC012687 | 16720154 | 1 | 19373 | 0 | 3160 | 22533 |
| S/G/Y/R/B/O |
NT_011754 | AC097262 | 16849365 | 1 | chrX | NT_011754 | AC107419 | 17455752 | 3 | 15626 | 0 | 0 | 15626 |
| S/G/Y/R/B/O |
NT_011754 | AC097262 | 16849365 | 1 | chrX | NT_011754 | AC113222 | 16962465 | 1 | 45911 | 0 | 13159 | 59070 |
| S/G/Y/R/B/O |
NT_011754 | AC017025 | 16852725 | 1 | chrX | NT_011754 | AC113222 | 16962465 | 1 | 43029 | 0 | 11125 | 54154 |
| S/G/Y/R/B/O |
NT_011754 | AC017025 | 16852725 | 1 | chrX | NT_011754 | AC012687 | 16720154 | 1 | 11338 | 0 | 15943 | 27281 |
| S/G/Y/R/B/O |
NT_011754 | AC017025 | 16852725 | 1 | chrX | NT_011754 | AC112493 | 16720942 | 3 | 31258 | 2183 | 0 | 33441 |
| S/G/Y/R/B/O |
NT_011754 | AC113222 | 16962465 | 1 | chrX | NT_011754 | AC084351 | 16982821 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011754 | AC113222 | 16962465 | 1 | chrX | NT_011754 | AC097262 | 16849365 | 1 | 45911 | 0 | 13159 | 59070 |
| S/G/Y/R/B/O |
NT_011754 | AC113222 | 16962465 | 1 | chrX | NT_011754 | AC107419 | 17455752 | 3 | 64422 | 0 | 19564 | 83986 |
| S/G/Y/R/B/O |
NT_011754 | AC113222 | 16962465 | 1 |   |   | AC055112 | 16852725 | 1 | 12726 | 12627 | 11580 | 36933 |
| S/G/Y/R/B/O |
NT_011754 | AC084351 | 16982821 | 1 | chrX | NT_011754 | AC112651 | 17021150 | 1 | 93585 | 7257 | 20037 | 120879 |
| S/G/Y/R/B/O |
NT_011754 | AC112651 | 17021150 | 1 | chrX | NT_011754 | AC005704 | 17178392 | 3 | 24136 | 0 | 0 | 24136 |
| S/G/Y/R/B/O |
NT_011754 | AC005704 | 17178392 | 3 | chrX | NT_011754 | AC073583 | 17234247 | 3 | 43116 | 0 | 0 | 43116 |
| S/G/Y/R/B/O |
NT_011754 | AC005704 | 17178392 | 3 |   |   | AC112652 | 17021150 | 1 | 79222 | 0 | 1957 | 81179 |
| S/G/Y/R/B/O |
NT_011754 | AC073583 | 17234247 | 3 | chrX | NT_011754 | AC107419 | 17455752 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011754 | AC073583 | 17234247 | 3 |   |   | AC112652 | 17178392 | 1 | 133764 | 0 | 27040 | 160804 |
| S/G/Y/R/B/O |
NT_011754 | AC107419 | 17455752 | 3 | chrX | NT_011754 | AC006210 | 17607652 | 3 | 2039 | 0 | 0 | 2039 |
| S/G/Y/R/B/O |
NT_011754 | AC107419 | 17455752 | 3 | chrX | NT_011754 | AC097262 | 16849365 | 1 | 15626 | 0 | 0 | 15626 |
| S/G/Y/R/B/O |
NT_011754 | AC107419 | 17455752 | 3 | chrX | NT_011754 | AC113222 | 16962465 | 1 | 64422 | 0 | 19564 | 83986 |
| S/G/Y/R/B/O |
NT_011754 | AC006210 | 17607652 | 3 | chrX | NT_011754 | AC079902 | 17791254 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011754 | AC006210 | 17607652 | 3 | chrX | NT_011754 | AC025065 | 17880636 | 1 | 77656 | 570 | 0 | 78226 |
| S/G/Y/R/B/O |
NT_011754 | AC079902 | 17791254 | 3 | chrX | NT_011754 | AC025065 | 17880636 | 1 | 70598 | 4334 | 0 | 74932 |
| S/G/Y/R/B/O |
NT_011754 | AC079902 | 17791254 | 3 | chrX | NT_011754 | AC107613 | 17896801 | 1 | 50492 | 0 | 0 | 50492 |
| S/G/Y/R/B/O |
NT_011754 | AC025065 | 17880636 | 1 | chrX | NT_011754 | AC107613 | 17896801 | 1 | 60202 | 4894 | 0 | 65096 |
| S/G/Y/R/B/O |
NT_011754 | AC025065 | 17880636 | 1 | chrX | NT_011754 | AC006210 | 17607652 | 3 | 77656 | 570 | 0 | 78226 |
| S/G/Y/R/B/O |
NT_011754 | AC107613 | 17896801 | 1 | chrX | NT_011754 | AC003659 | 18042305 | 1 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011754 | AC107613 | 17896801 | 1 | chrX | NT_011754 | AC011693 | 18489589 | 1 | 127073 | 0 | 0 | 127073 |
| S/G/Y/R/B/O |
NT_011754 | AC107613 | 17896801 | 1 | chrX | NT_011754 | AC018862 | 18476115 | 1 | 82881 | 7587 | 14895 | 105363 |
| S/G/Y/R/B/O |
NT_011754 | AC107613 | 17896801 | 1 | chrX | NT_011754 | AC021710 | 18458769 | 1 | 11550 | 0 | 0 | 11550 |
| S/G/Y/R/B/O |
NT_011754 | AC107613 | 17896801 | 1 | chrX | NT_011754 | AC079902 | 17791254 | 3 | 50492 | 0 | 0 | 50492 |
| S/G/Y/R/B/O |
NT_011754 | AC003659 | 18042305 | 1 | chrX | NT_011754 | AC003667 | 18074491 | 3 | 0 | 0 | 6838 | 6838 |
| S/G/Y/R/B/O |
NT_011754 | AC003659 | 18042305 | 1 | chrX | NT_011754 | AC023037 | 15203342 | 1 | 10575 | 23094 | 36231 | 69900 |
| S/G/Y/R/B/O |
NT_011754 | AC003667 | 18074491 | 3 | chrX | NT_011754 | AC112916 | 18206506 | 3 | 2003 | 0 | 0 | 2003 |
| S/G/Y/R/B/O |
NT_011754 | AC003667 | 18074491 | 3 | chrX | NT_011754 | AC025239 | 15197919 | 1 | 61732 | 4072 | 3186 | 68990 |
| S/G/Y/R/B/O |
NT_011754 | AC112916 | 18206506 | 3 | chrX | NT_011754 | AC004553 | 18378110 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_011754 | AC112916 | 18206506 | 3 | chrX | NT_011754 | AC025239 | 15197919 | 1 | 41350 | 2954 | 36845 | 81149 |
| S/G/Y/R/B/O |
NT_011754 | AC112916 | 18206506 | 3 |   |   | AC097348 | 15197919 | 3 | 85274 | 0 | 0 | 85274 |
| S/G/Y/R/B/O |
NT_011754 | AC004553 | 18378110 | 3 | chrX | NT_011754 | AC021710 | 18458769 | 1 | 26850 | 0 | 53121 | 79971 |
| S/G/Y/R/B/O |
NT_011754 | AC004553 | 18378110 | 3 | chrX | NT_011754 | AC112492 | 18683055 | 1 | 51935 | 2669 | 6373 | 60977 |
| S/G/Y/R/B/O |
NT_011754 | AC021710 | 18458769 | 1 | chrX | NT_011754 | AC018862 | 18476115 | 1 | 38433 | 0 | 0 | 38433 |
| S/G/Y/R/B/O |
NT_011754 | AC021710 | 18458769 | 1 | chrX | NT_011754 | AC011693 | 18489589 | 1 | 42484 | 1778 | 0 | 44262 |
| S/G/Y/R/B/O |
NT_011754 | AC021710 | 18458769 | 1 | chrX | NT_011754 | AC107613 | 17896801 | 1 | 11550 | 0 | 0 | 11550 |
| S/G/Y/R/B/O |
NT_011754 | AC021710 | 18458769 | 1 | chrX | NT_011754 | AC112492 | 18683055 | 1 | 99064 | 23274 | 27341 | 149679 |
| S/G/Y/R/B/O |
NT_011754 | AC018862 | 18476115 | 1 | chrX | NT_011754 | AC011693 | 18489589 | 1 | 75439 | 7586 | 2414 | 85439 |
| S/G/Y/R/B/O |
NT_011754 | AC018862 | 18476115 | 1 | chrX | NT_011754 | AC107613 | 17896801 | 1 | 82881 | 7587 | 14895 | 105363 |
| S/G/Y/R/B/O |
NT_011754 | AC011693 | 18489589 | 1 | chrX | NT_011754 | AC112492 | 18683055 | 1 | 11526 | 13628 | 7258 | 32412 |
| S/G/Y/R/B/O |
NT_011754 | AC011693 | 18489589 | 1 | chrX | NT_011754 | AC021710 | 18458769 | 1 | 42484 | 1778 | 0 | 44262 |
| S/G/Y/R/B/O |
NT_011754 | AC011693 | 18489589 | 1 | chrX | NT_011754 | AC107613 | 17896801 | 1 | 127073 | 0 | 0 | 127073 |
| S/G/Y/R/B/O |
NT_011754 | AC112492 | 18683055 | 1 |   |   |   |   |   |   |   |   |   |
| S/G/Y/R/B/O |
NT_011754 | AC112492 | 18683055 | 1 | chrX | NT_011754 | AC004553 | 18378110 | 3 | 51935 | 2669 | 6373 | 60977 |
| S/G/Y/R/B/O |
NT_011754 | AC112492 | 18683055 | 1 | chrX | NT_011754 | AC021710 | 18458769 | 1 | 99064 | 23274 | 27341 | 149679 |
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