Table 1.
DraI SNP primers, locations and band sizes. In each pair of primers, the left primer is listed first; all primer sequences are given 5' to 3'. Interpolated genetic positions are from [9] release WS143.
| Genetic Location | Physical Location | Clone | N2 digest | CB4856 digest | Primers | Wormbase Identifier |
| I, -19 | 169, 017 | F56C11 | 354, 146 | 500 | ATGCCAGTGATAAGGAACGG | snp_F56C11 [4] |
| TCACATCCCTTGTCGATGAA | ||||||
| I, -12 | 1,905,969 | Y71G12A | 503, 72 | 377, 126, 72 | TCGAAATCAGGGAAAAATTGA | snp_Y71G12 [3] |
| ACGATTTTCGGGGAGTTTTT | ||||||
| I, -6 | 2,818,973 | W03D8 | 395, 144 | 538 | GTTTTCACTTTTGCCGGTGT | pkP1052 |
| TGAAGGCGCATATACAGCAG | ||||||
| I, -1 | 4,594,014 | D1007 | 325, 134, 41 | 459, 41 | AAAATATCAGGAAAGAGTTTCGG | snp_D1007 [7] |
| TTTAAAGATTAAGGGTGGAGCG | ||||||
| I, 5 | 10,722,146 | B0205 | 494 | 365, 129 | ATCTGGCACCAAATATGAGTCG | CE1-247 |
| AATCTCGATTTTCAAGGAGTGG | (rs3139013)** | |||||
| I, 13 | 12,047,594 | F58D5 | 445 | 295, 151 | TCCTGGATAATCCCCAAAAA | snp_F58D5 [4] |
| CCCTGCCATTGATCTTGTTT | ||||||
| I, 14 | 12,729,812 | T06G6 | 236, 99, 78 | 335, 78 | TTGAAATCCCCTTTAAAATCCC | uCE1-1361 |
| ACACTGGGTACCTGACTCATGC | ||||||
| I, 26 | 14,682,016 | Y105E8B | 360, 114, 27 | 474, 27 | ATTATTAACGGCCACGGTGA | snp_Y105E8B [3] |
| CCCACACACTCTCACCTTCA | ||||||
| II, -18 | 176,720 | T01D1 | 263, 112 | 375 | CCGAATTTTCAAATGGATGC | pkP2101 |
| CCATTGGAATTGCACACAAA | ||||||
| II, -14 | 2,121,018 | R52 | 345 | 236, 109 | CTGTGCTGTTGACGATATTGG | snp_R52 [5] |
| ATGTCTCATTGCAAAATTCGG | ||||||
| II, -6 | 3,828,599 | F54D10 | 516 | 387, 129 | TTGTGAGCTTATATCTCAGTTGTCG | pkP2103 |
| AGATTTGGTTAGAAATATCACCGC | ||||||
| II, 1 | 9,052,466 | T24B8 | 373, 121 | 494 | TCAAAAACTTACAATCAATCGTCG | snp_T24B8 [1] |
| CCAGAAAATCTGCACAGAAGG | ||||||
| II, 4 | 11,827,835 | Y6D1A | 224, 117, 124, 44 | 340, 124, 44 | TTCTTCAAAAAGTCTAGGTTCAGCA | snp_Y6D1 [1] |
| GGGGACGAAAACGGAGTTTG | ||||||
| II, 11 | 12,605,350 | Y38E10A | 483 | 352, 132 | ACCGTTTAATAGGATTATTTGGG | uCE2-2131 |
| AAGTCTGCGGAATAATTGATGG | ||||||
| II, 16 | 13,235,564 | F15D4 | 500 | 368, 132 | TTCCAGGTAATACACATACAACTCC | pkP2116 |
| AAAAACACAAAGTTCAAAAACCC | ||||||
| II, 22 | 14,132,466 | K09E4 | 365, 119 | 484 | CCACTGGCTATAAGCTTTTCTAGG | CE2-215 |
| TAAGGATTTCAGGCTTTTAGGC | (rs3139227)** | |||||
| III, -25 | 939,698 | T12B5 | 206, 189 | 395 | TATCATCGAAATCCCGGAAA | uCE3-637 |
| TTCGGACGGGAGTAGAATTG | ||||||
| III, -19 | 1,827,732 | Y39A3CL | 342, 78, 76 | 272, 78, 76, 70 | TCCCAATTTCCCTCTAAAAACC | uCE3-735 |
| TTGAATTTGGACCATTTTGAGG | ||||||
| III, -12 | 2,599,699 | Y71H2B | 368, 105 | 473 | GAGGAACCAAATCTGGCGTA | snp_Y71H2B [2] |
| TGAAAACTTGGAAAATCGGTG | ||||||
| III, -7 | 3,359,033 | F45H7 | 239, 85, 27 | 196, 85, 43, 27 | AATTTGAATCAGTGACTTTTGGC | CE3-127 |
| TTTCTGCAAACATTTTTCTTCG | (rs3139272)** | |||||
| III, -1 | 7,320,107 | F56C9 | 486 | 354, 132 | AAAAATACATGTCTACACAACCCG | snp_F56C9 [1] |
| TTTCTTATCACTGTGCAGTCTTACC | ||||||
| III, 4 | 10,652,476 | Y39A1A | 355, 142, 30 | 497, 30 | AGCGTTAAAGTATCGGTTATTTCG | snp_Y39A1 [9] |
| TAAATTCATTTCAAACAATCGAGC | ||||||
| III, 12 | 11,656,188 | Y41C4A | 339, 156 | 495 | ATCAAGTTTCTGATTGCTCTTTCC | snp_Y41C4 [2] |
| AAAAACGTGATTTTTCAATTTTGC | ||||||
| III, +21 | 13,715,622 | W06F12 | 273, 137, 78 | 200, 137, 78, 73 | AGCAGGCTCACCATCATCATCA | uCE3-1426 |
| GACATTACGGTAGAGGAGATGGA | ||||||
| IV, -24 | 795,461 | F56B3 | 301, 128, 71 | 429, 71 | TGATGGTGTGTCTGCGTACC | uCE4-515 |
| AGAGCTGGAGAGCACGGATA | ||||||
| IV, -16 | 1,799,032 | Y38C1BA | 187, 304 | 491 | CGCATAAATCCAACGTTCTCTG | snp_Y38C1B [2] |
| AATCCATAAGTTTCGTGTTGGG | ||||||
| IV, -7 | 2,761,525 | Y54G2A | 498 | 250, 248 | ACTCGGCATCCTCACGC | snp_Y54G2 [5] |
| GTTGAAAATTTTTTCATAGCTATCATC | ||||||
| IV, -5 | 3,347,952 | F42A6 | 295, 124 | 419 | TGCTGAAATATTGGAAAATTGAGG | pkP4055 |
| TTATATCGTCGAGGAGGTTAGAGG | ||||||
| IV, 1 | 4,991,851 | E03H12 | 376 | 300, 76 | AAAATGGGAAGCGTACCAAA | pkP4071 |
| TGCTTGTAGCGTTTCCAAGA | ||||||
| IV, 8 | 13,049,020 | F49E11 | 313, 77 | 390 | GACACGACTTTAGAAACAACAGC | snp_F49E11 [1] |
| TGGTATGGAGTCCCTATTTTGG | ||||||
| IV, 12 | 14,566,396 | Y57G11B | 284, 162, 52* | 327, 119, 52* | TGTAAATACCCCACATTTCAAGC | snp_Y57G11B [2] |
| AAATTTCCAATTGTTCAAAGCC | pkP4095* | |||||
| IV, 14 | 16,085,085 | Y105C5B | 241, 108, 78, 48 | 319, 108, 48 | TCGAATTGTTGTGTTTCTTTTGA | pkP4099 |
| TTCCAATTTTCTCGGTTTGG | ||||||
| V, -17 | 1,773,464 | F36H9 | 307, 87, 79 | 386, 87 | TTTCGGAAAATTGCGACTGT | pkP5076 |
| CGCGTTTTGGAGAATTGTTT | ||||||
| V, -13 | 2,726,662 | C24B9 | 288, 167 | 455 | TCATCTGTTATTTCGTCTCTTGC | uCE5-828 |
| CGGTAATAATATGCTTTGTGGG | ||||||
| V, -5 | 4,550,757 | Y61A9LA | 454 | 307, 147 | GAGATTCTAGAGAAATGGACACCC | snp_Y61A9L [1] |
| AAAAATCGACTACACCACTTTTAGC | ||||||
| V, 1 | 7,089,411 | VC5 | 435, 70 | 300, 135, 70 | AGAAATGATCCGATGAAAAAGC | pkP5097 |
| CCGATAGTGTTCATAGCATCCC | ||||||
| V, 6 | 13,951,850 | R10D12 | 500 | 348, 152 | CAAATTAAATATTTCTCAAAGTTTCGG | *** |
| ACATAAGCGCCATAACAAGTCG | ||||||
| V, 10 | 16,321,481 | F57G8 | 475 | 288, 187 | TAAAGCCGCTACGGAAATACTC | pkP5129 |
| ATTTTCTCCCTAATTCCAGGTG | ||||||
| V, 13 | 17,610,508 | Y6G8 | 282, 205 | 487 | CATTCATTTCACCTGTTGGTTG | uCE5-2609 |
| TCGGGAAGATAATCAAAATTCG | ||||||
| V, 18 | 18,782,547 | Y17D7B | 324, 164 | 488 | GAAATTCAAATTTTTGAGAAACCC | snp_Y17D7B [3] |
| TTCAGACCATTTTTAGAATATTCAGG | ||||||
| X, -17 | 2,065,464 | F49H12 | 540 | 321, 219 | ATATGTGAGTTTACCATCACTGGG | pkP6143 |
| ACGTTTTGAAAAATTTGGTTGC | ||||||
| X, -8 | 4,161,493 | ZK470 | 422, 72, 40 | 326, 96, 72, 40 | CCAAAACGGCCAAGTATCAG | pkP6105 |
| TTGCACTCTTTCTCCTTCCG | ||||||
| X, -4 | 5,934,688 | C46F4 | 169, 54, 51, 35, 22 | 223, 51, 35, 22 | AAGTGTTCAATGATTTTGTCTAATTG | uCE6-981 |
| TGACAGGAGAATACTTTTGAAGG | ||||||
| X, 2 | 10,637,922 | F11A1 | 409, 133 | 542 | AGCAACAAACAATGCAACTATGG | snp_F11A1 [2] |
| TAAACAAGAGGGTACAAGGTATCG | ||||||
| X, 8 | 12,750,713 | F22E10 | 341, 126 | 467 | TTAAAACCATACAATTCTTCTCAGC | snp_F22E10 [1] |
| GAATTCCCAATCAACAGAGAGC | ||||||
| X, 11 | 13,339,566 | F46G10 | 318, 191, 37 | 509, 37 | ACTGTTTACCGCGTCTTCTGC | pkP6132 |
| CCGTGTATATAAGAAAATGTGTTCG | ||||||
| X, 17 | 14,547,382 | T24C2 | 409, 34 | 302, 107, 34 | GCTGGGATTTTGAAGAGTTGTT | uCE6-1459 |
| CAGTGAATCATCCGTTGAATTT | ||||||
| X, 23 | 15,500,013 | H13N06 | 358, 134 | 492 | CAAATACCAAAGTTGATCGTGG | uCE6-1554 |
| TTGTTGCAATTAAATCAAACGG |
*Y57G11B has two DraI SNPs within a single PCR product.
**dbSNP IDs are given where the SNP has been submitted to the NCBI dbSNP database [10].
***The SNP on R10D12 has not been added to wormbase. It can be found at [11]