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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_026239 | AC016171 | 54441822 | 1 | chr2 | NT_026239 | AC096583 | 54449442 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_026239 | AC016171 | 54441822 | 1 | chr2 | NT_026239 | AC013414 | 56698783 | 3 | 32063 | 0 | 0 | 32063 |
| S/G/Y/R/B/O |
NT_026239 | AC016171 | 54441822 | 1 | chr2 | NT_026239 | AC092461 | 56860173 | 3 | 39010 | 0 | 0 | 39010 |
| S/G/Y/R/B/O |
NT_026239 | AC016171 | 54441822 | 1 | chr2 | NT_026239 | AC093165 | 56897847 | 3 | 81625 | 10377 | 1289 | 93291 |
| S/G/Y/R/B/O |
NT_026239 | AC096583 | 54449442 | 3 | chr2 | NT_026239 | AC019196 | 54501610 | 3 | 0 | 1999 | 0 | 1999 |
| S/G/Y/R/B/O |
NT_026239 | AC019196 | 54501610 | 3 | chr2 | NT_026239 | AC018713 | 54675113 | 3 | 0 | 1994 | 0 | 1994 |
| S/G/Y/R/B/O |
NT_026239 | AC018713 | 54675113 | 3 | chr2 | NT_026239 | AC010967 | 54689354 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_026239 | AC018713 | 54675113 | 3 |   |   | AC037488 | 54501610 | 1 | 13276 | 0 | 0 | 13276 |
| S/G/Y/R/B/O |
NT_026239 | AC010967 | 54689354 | 3 | chr2 | NT_026239 | AC016714 | 54884682 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_026239 | AC010967 | 54689354 | 3 |   |   | AC037488 | 54501610 | 1 | 177083 | 4955 | 8816 | 190854 |
| S/G/Y/R/B/O |
NT_026239 | AC016714 | 54884682 | 3 | chr2 | NT_026239 | AC009490 | 54940530 | 3 | 0 | 0 | 200 | 200 |
| S/G/Y/R/B/O |
NT_026239 | AC009490 | 54940530 | 3 | chr2 | NT_026239 | AC009241 | 55099022 | 3 | 0 | 0 | 200 | 200 |
| S/G/Y/R/B/O |
NT_026239 | AC009241 | 55099022 | 3 | chr2 | NT_026239 | AC069157 | 55270745 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_026239 | AC009241 | 55099022 | 3 |   |   | AC025315 | 54940530 | 1 | 24994 | 2202 | 0 | 27196 |
| S/G/Y/R/B/O |
NT_026239 | AC069157 | 55270745 | 3 | chr2 | NT_026239 | AC008064 | 55406774 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_026239 | AC069157 | 55270745 | 3 |   |   | AC025315 | 54940530 | 1 | 100729 | 14390 | 4817 | 119936 |
| S/G/Y/R/B/O |
NT_026239 | AC069157 | 55270745 | 3 |   |   | AC092433 | 54940530 | 1 | 138028 | 0 | 0 | 138028 |
| S/G/Y/R/B/O |
NT_026239 | AC008064 | 55406774 | 3 | chr2 | NT_026239 | AC007883 | 55577353 | 3 | 0 | 0 | 200 | 200 |
| S/G/Y/R/B/O |
NT_026239 | AC008064 | 55406774 | 3 |   |   | AC025315 | 55577353 | 1 | 13532 | 4427 | 1902 | 19861 |
| S/G/Y/R/B/O |
NT_026239 | AC008064 | 55406774 | 3 |   |   | AC092433 | 55577353 | 1 | 34505 | 0 | 0 | 34505 |
| S/G/Y/R/B/O |
NT_026239 | AC007883 | 55577353 | 3 | chr2 | NT_026239 | AC008068 | 55690342 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_026239 | AC008068 | 55690342 | 3 | chr2 | NT_026239 | AC008280 | 55844178 | 3 | 0 | 0 | 200 | 200 |
| S/G/Y/R/B/O |
NT_026239 | AC008280 | 55844178 | 3 | chr2 | NT_026239 | AC092622 | 56024573 | 3 | 2000 | 0 | 0 | 2000 |
| S/G/Y/R/B/O |
NT_026239 | AC092622 | 56024573 | 3 | chr2 | NT_026239 | AC073879 | 56042104 | 3 | 2000 | 0 | 0 | 2000 |
| S/G/Y/R/B/O |
NT_026239 | AC092622 | 56024573 | 3 |   |   | AC023393 | 55844178 | 1 | 13598 | 0 | 0 | 13598 |
| S/G/Y/R/B/O |
NT_026239 | AC073879 | 56042104 | 3 | chr2 | NT_026239 | AC108929 | 56228285 | 3 | 96787 | 0 | 0 | 96787 |
| S/G/Y/R/B/O |
NT_026239 | AC073879 | 56042104 | 3 |   |   | AC023393 | 56042104 | 1 | 160242 | 1761 | 0 | 162003 |
| S/G/Y/R/B/O |
NT_026239 | AC108929 | 56228285 | 3 | chr2 | NT_026239 | AC092839 | 56241525 | 3 | 0 | 1999 | 0 | 1999 |
| S/G/Y/R/B/O |
NT_026239 | AC108929 | 56228285 | 3 |   |   | AC023393 | 56228285 | 1 | 26225 | 0 | 0 | 26225 |
| S/G/Y/R/B/O |
NT_026239 | AC092839 | 56241525 | 3 | chr2 | NT_026239 | AC093110 | 56425989 | 3 | 2000 | 0 | 0 | 2000 |
| S/G/Y/R/B/O |
NT_026239 | AC093110 | 56425989 | 3 | chr2 | NT_026239 | AC104781 | 56592539 | 1 | 62267 | 0 | 0 | 62267 |
| S/G/Y/R/B/O |
NT_026239 | AC093110 | 56425989 | 3 |   |   | AC011187 | 56228285 | 1 | 29361 | 0 | 0 | 29361 |
| S/G/Y/R/B/O |
NT_026239 | AC093110 | 56425989 | 3 |   |   | AC023927 | 56228285 | 1 | 32921 | 1988 | 1437 | 36346 |
| S/G/Y/R/B/O |
NT_026239 | AC093110 | 56425989 | 3 |   |   | AC040988 | 56228285 | 1 | 93849 | 4983 | 1471 | 100303 |
| S/G/Y/R/B/O |
NT_026239 | AC104781 | 56592539 | 1 | chr2 | NT_026239 | AC013414 | 56698783 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_026239 | AC104781 | 56592539 | 1 |   |   | AC011187 | 56592539 | 1 | 126286 | 0 | 2319 | 128605 |
| S/G/Y/R/B/O |
NT_026239 | AC104781 | 56592539 | 1 |   |   | AC011211 | 56592539 | 1 | 85319 | 0 | 0 | 85319 |
| S/G/Y/R/B/O |
NT_026239 | AC104781 | 56592539 | 1 |   |   | AC023927 | 56592539 | 1 | 85612 | 1991 | 2639 | 90242 |
| S/G/Y/R/B/O |
NT_026239 | AC104781 | 56592539 | 1 |   |   | AC040988 | 56592539 | 1 | 103390 | 5659 | 1882 | 110931 |
| S/G/Y/R/B/O |
NT_026239 | AC104781 | 56592539 | 1 |   |   | AC097456 | 56425989 | 1 | 85271 | 0 | 0 | 85271 |
| S/G/Y/R/B/O |
NT_026239 | AC013414 | 56698783 | 3 | chr2 | NT_026239 | AC092461 | 56860173 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_026239 | AC013414 | 56698783 | 3 | chr2 | NT_026239 | AC016171 | 54441822 | 1 | 32063 | 0 | 0 | 32063 |
| S/G/Y/R/B/O |
NT_026239 | AC013414 | 56698783 | 3 |   |   | AC011187 | 56425989 | 1 | 14230 | 0 | 1241 | 15471 |
| S/G/Y/R/B/O |
NT_026239 | AC013414 | 56698783 | 3 |   |   | AC011211 | 56425989 | 1 | 80373 | 0 | 0 | 80373 |
| S/G/Y/R/B/O |
NT_026239 | AC013414 | 56698783 | 3 |   |   | AC097456 | 54441822 | 1 | 80373 | 0 | 0 | 80373 |
| S/G/Y/R/B/O |
NT_026239 | AC092461 | 56860173 | 3 | chr2 | NT_026239 | AC093165 | 56897847 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_026239 | AC092461 | 56860173 | 3 | chr2 | NT_026239 | AC016171 | 54441822 | 1 | 39010 | 0 | 0 | 39010 |
| S/G/Y/R/B/O |
NT_026239 | AC093165 | 56897847 | 3 | chr2 | NT_026239 | AC012358 | 57059619 | 3 | 2000 | 0 | 0 | 2000 |
| S/G/Y/R/B/O |
NT_026239 | AC093165 | 56897847 | 3 | chr2 | NT_026239 | AC016171 | 54441822 | 1 | 81625 | 10377 | 1289 | 93291 |
| S/G/Y/R/B/O |
NT_026239 | AC012358 | 57059619 | 3 | chr2 | NT_026239 | AC092176 | 57219770 | 3 | 0 | 1999 | 0 | 1999 |
| S/G/Y/R/B/O |
NT_026239 | AC012358 | 57059619 | 3 |   |   | AC016242 | 54441822 | 1 | 71205 | 6189 | 39423 | 116817 |
| S/G/Y/R/B/O |
NT_026239 | AC092176 | 57219770 | 3 | chr2 | NT_026239 | AC019198 | 57235071 | 3 | 0 | 1998 | 0 | 1998 |
| S/G/Y/R/B/O |
NT_026239 | AC092176 | 57219770 | 3 |   |   | AC016242 | 57059619 | 1 | 16904 | 0 | 0 | 16904 |
| S/G/Y/R/B/O |
NT_026239 | AC019198 | 57235071 | 3 | chr2 | NT_026239 | AC015982 | 57384126 | 3 | 2000 | 0 | 0 | 2000 |
| S/G/Y/R/B/O |
NT_026239 | AC019198 | 57235071 | 3 |   |   | AC016242 | 57384126 | 1 | 26660 | 0 | 0 | 26660 |
| S/G/Y/R/B/O |
NT_026239 | AC015982 | 57384126 | 3 | chr2 | NT_026239 | AC023343 | 57573672 | 3 | 0 | 0 | 200 | 200 |
| S/G/Y/R/B/O |
NT_026239 | AC023343 | 57573672 | 3 | chr2 | NT_026239 | AC010895 | 57577812 | 3 | 0 | 0 | 200 | 200 |
| S/G/Y/R/B/O |
NT_026239 | AC010895 | 57577812 | 3 | chr2 | NT_026239 | AC096549 | 57777975 | 3 | 2000 | 0 | 0 | 2000 |
| S/G/Y/R/B/O |
NT_026239 | AC096549 | 57777975 | 3 | chr2 | NT_026239 | AC104661 | 57813214 | 3 | 2000 | 0 | 0 | 2000 |
| S/G/Y/R/B/O |
NT_026239 | AC104661 | 57813214 | 3 | chr2 | NT_026239 | AC011306 | 57817330 | 3 | 0 | 1996 | 0 | 1996 |
| S/G/Y/R/B/O |
NT_026239 | AC011306 | 57817330 | 3 | chr2 | NT_026239 | AC007743 | 57985433 | 3 | 2000 | 0 | 0 | 2000 |
| S/G/Y/R/B/O |
NT_026239 | AC007743 | 57985433 | 3 | chr2 | NT_026239 | AC007744 | 58125269 | 3 | 0 | 0 | 200 | 200 |
| S/G/Y/R/B/O |
NT_026239 | AC007744 | 58125269 | 3 | chr2 | NT_026239 | AC009507 | 58324287 | 3 | 0 | 0 | 200 | 200 |
| S/G/Y/R/B/O |
NT_026239 | AC009507 | 58324287 | 3 | chr2 | NT_026239 | AC008173 | 58446300 | 3 | 0 | 0 | 200 | 200 |
| S/G/Y/R/B/O |
NT_026239 | AC008173 | 58446300 | 3 | chr2 | NT_026239 | AC007971 | 58639993 | 3 | 0 | 0 | 0 | 0 |
| S/G/Y/R/B/O |
NT_026239 | AC008173 | 58446300 | 3 |   |   | AC068815 | 58324287 | 1 | 23078 | 5919 | 1082 | 30079 |
| S/G/Y/R/B/O |
NT_026239 | AC007971 | 58639993 | 3 | chr2 | NT_026239 | AC096584 | 58786498 | 3 | 2000 | 0 | 0 | 2000 |
| S/G/Y/R/B/O |
NT_026239 | AC007971 | 58639993 | 3 |   |   | AC068815 | 58324287 | 1 | 130996 | 2793 | 4262 | 138051 |
| S/G/Y/R/B/O |
NT_026239 | AC096584 | 58786498 | 3 | chr2 | NT_026239 | AC010738 | 58800170 | 3 | 2000 | 0 | 0 | 2000 |
| S/G/Y/R/B/O |
NT_026239 | AC010738 | 58800170 | 3 | chr2 | NT_026239 | AC009406 | 58919618 | 3 | 0 | 0 | 200 | 200 |
| S/G/Y/R/B/O |
NT_026239 | AC009406 | 58919618 | 3 | chr2 | NT_026239 | AC108023 | 59076235 | 3 | 2000 | 0 | 0 | 2000 |
| S/G/Y/R/B/O |
NT_026239 | AC108023 | 59076235 | 3 |   |   |   |   |   |   |   |   |   |
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