{ "about": { "generatedBy": "pipeline/plasmid-map/reference.py", "scriptSha256": "0d7026c8338f04ccc78bc8d477a61d211787e4473326d4c28ed9ba62924875ff", "recordedOn": "2026-10-06", "oracle": "Biopython 1.88", "oracleLicence": "Biopython Licence Agreement or BSD-3-Clause", "text": "Cut positions of every enzyme in the table on pUC19 (L09137.2, 2,686 bp, circular) and pBR322 (J01749.1, 4,361 bp, circular), from Biopython's search(linear=False): the 1-based position of the first base after the top-strand cut. Fragments are the circular single digests' lengths in bp. The golden set carries the REBASE page's count of sites on pBR322, read by hand; NEBcutter 3's column is null, to be recorded by hand.", "rebaseRelease": "404", "goldenSet": [ "AatII", "AflIII", "AlwNI", "ApaLI", "AvaI", "BamHI", "BbsI", "BbvCI", "BglI", "BsaI", "BsmBI", "BspHI", "BtgI", "ClaI", "DraI", "EcoO109I", "EcoRI", "EcoRII", "EcoRV", "FspI", "HincII", "HindIII", "KpnI", "MboI", "NdeI", "NheI", "NruI", "PciI", "PstI", "PvuI", "PvuII", "SacI", "SalI", "SapI", "ScaI", "SmaI", "SphI", "SspI", "XbaI", "XmnI" ], "goldenAgreeWithRebasePages": true }, "plasmids": { "L09137.2": { "length": 2686, "circular": true }, "J01749.1": { "length": 4361, "circular": true } }, "cases": [ { "enzyme": "AarI", "plasmid": "L09137.2", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "AarI", "plasmid": "J01749.1", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "AatII", "plasmid": "L09137.2", "cuts": [ 2622 ], "count": 1, "fragments": [ 2686 ] }, { "enzyme": "AatII", "plasmid": "J01749.1", "cuts": [ 4289 ], "count": 1, "fragments": [ 4361 ], "rebasePage": { "recognition": "GACGT^C", "sitesOnPBR322": 1, "readOn": "2026-10-06", "agrees": true }, "nebcutter": null }, { "enzyme": "AbsI", "plasmid": "L09137.2", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "AbsI", "plasmid": "J01749.1", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "Acc65I", "plasmid": "L09137.2", "cuts": [ 409 ], "count": 1, "fragments": [ 2686 ] }, { "enzyme": "Acc65I", "plasmid": "J01749.1", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "AccI", "plasmid": "L09137.2", "cuts": [ 431 ], "count": 1, "fragments": [ 2686 ] }, { "enzyme": "AccI", "plasmid": "J01749.1", "cuts": [ 653, 2246 ], "count": 2, "fragments": [ 2768, 1593 ] }, { "enzyme": "AciI", "plasmid": "L09137.2", "cuts": [ 76, 115, 125, 151, 189, 202, 228, 285, 497, 600, 656, 666, 690, 733, 740, 761, 852, 880, 1007, 1026, 1147, 1257, 1392, 1401, 1763, 1854, 2045, 2091, 2212, 2256, 2333, 2442, 2541, 2588 ], "count": 34, "fragments": [ 362, 212, 191, 174, 135, 127, 121, 121, 110, 109, 103, 99, 91, 91, 77, 57, 56, 47, 46, 44, 43, 39, 38, 28, 26, 26, 24, 21, 19, 13, 10, 10, 9, 7 ] }, { "enzyme": "AciI", "plasmid": "J01749.1", "cuts": [ 40, 182, 290, 299, 302, 426, 579, 582, 585, 704, 724, 803, 843, 892, 939, 1024, 1039, 1107, 1140, 1165, 1210, 1234, 1246, 1288, 1342, 1395, 1411, 1417, 1498, 1636, 1765, 1768, 1779, 1935, 1951, 2006, 2062, 2147, 2186, 2196, 2238, 2263, 2301, 2314, 2340, 2357, 2400, 2407, 2428, 2519, 2547, 2674, 2693, 2814, 2924, 3059, 3068, 3430, 3521, 3712, 3758, 3879, 3923, 4000, 4109, 4208, 4255 ], "count": 67, "fragments": [ 362, 191, 156, 153, 146, 142, 138, 135, 129, 127, 124, 121, 121, 119, 110, 109, 108, 99, 91, 91, 85, 85, 81, 79, 77, 68, 56, 55, 54, 53, 49, 47, 47, 46, 45, 44, 43, 42, 42, 40, 39, 38, 33, 28, 26, 25, 25, 24, 21, 20, 19, 17, 16, 16, 15, 13, 12, 11, 10, 9, 9, 7, 6, 3, 3, 3, 3 ] }, { "enzyme": "AclI", "plasmid": "L09137.2", "cuts": [ 1926, 2299 ], "count": 2, "fragments": [ 2313, 373 ] }, { "enzyme": "AclI", "plasmid": "J01749.1", "cuts": [ 902, 1801, 3593, 3966 ], "count": 4, "fragments": [ 1792, 1297, 899, 373 ] }, { "enzyme": "AcuI", "plasmid": "L09137.2", "cuts": [ 1355, 2367 ], "count": 2, "fragments": [ 1674, 1012 ] }, { "enzyme": "AcuI", "plasmid": "J01749.1", "cuts": [ 3022, 4034 ], "count": 2, "fragments": [ 3349, 1012 ] }, { "enzyme": "AfeI", "plasmid": "L09137.2", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "AfeI", "plasmid": "J01749.1", "cuts": [ 235, 497, 778, 1730 ], "count": 4, "fragments": [ 2866, 952, 281, 262 ] }, { "enzyme": "AflII", "plasmid": "L09137.2", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "AflII", "plasmid": "J01749.1", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "AflIII", "plasmid": "L09137.2", "cuts": [ 807 ], "count": 1, "fragments": [ 2686 ] }, { "enzyme": "AflIII", "plasmid": "J01749.1", "cuts": [ 2474 ], "count": 1, "fragments": [ 4361 ], "rebasePage": { "recognition": "A^CRYGT", "sitesOnPBR322": 1, "readOn": "2026-10-06", "agrees": true }, "nebcutter": null }, { "enzyme": "AgeI", "plasmid": "L09137.2", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "AgeI", "plasmid": "J01749.1", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "AhdI", "plasmid": "L09137.2", "cuts": [ 1700 ], "count": 1, "fragments": [ 2686 ] }, { "enzyme": "AhdI", "plasmid": "J01749.1", "cuts": [ 3367 ], "count": 1, "fragments": [ 4361 ] }, { "enzyme": "AleI", "plasmid": "L09137.2", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "AleI", "plasmid": "J01749.1", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "AluI", "plasmid": "L09137.2", "cuts": [ 45, 64, 309, 405, 450, 472, 567, 631, 749, 975, 1065, 1111, 1368, 1889, 1989, 2052 ], "count": 16, "fragments": [ 679, 521, 257, 245, 226, 118, 100, 96, 95, 90, 64, 63, 46, 45, 22, 19 ] }, { "enzyme": "AluI", "plasmid": "J01749.1", "cuts": [ 17, 32, 688, 1091, 1999, 2056, 2067, 2116, 2135, 2416, 2642, 2732, 2778, 3035, 3556, 3656, 3719 ], "count": 17, "fragments": [ 908, 659, 656, 521, 403, 281, 257, 226, 100, 90, 63, 57, 49, 46, 19, 15, 11 ] }, { "enzyme": "AlwI", "plasmid": "L09137.2", "cuts": [ 413, 426, 1368, 1454, 1456, 1552, 1553, 2016, 2333, 2337 ], "count": 10, "fragments": [ 942, 762, 463, 317, 96, 86, 13, 4, 2, 1 ] }, { "enzyme": "AlwI", "plasmid": "J01749.1", "cuts": [ 371, 384, 1106, 1676, 3035, 3121, 3123, 3219, 3220, 3683, 4000, 4004 ], "count": 12, "fragments": [ 1359, 728, 722, 570, 463, 317, 96, 86, 13, 4, 2, 1 ] }, { "enzyme": "AlwNI", "plasmid": "L09137.2", "cuts": [ 1223 ], "count": 1, "fragments": [ 2686 ] }, { "enzyme": "AlwNI", "plasmid": "J01749.1", "cuts": [ 2890 ], "count": 1, "fragments": [ 4361 ], "rebasePage": { "recognition": "CAGNNN^CTG", "sitesOnPBR322": 1, "readOn": "2026-10-06", "agrees": true }, "nebcutter": null }, { "enzyme": "ApaI", "plasmid": "L09137.2", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "ApaI", "plasmid": "J01749.1", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "ApaLI", "plasmid": "L09137.2", "cuts": [ 178, 1121, 2367 ], "count": 3, "fragments": [ 1246, 943, 497 ] }, { "enzyme": "ApaLI", "plasmid": "J01749.1", "cuts": [ 2290, 2788, 4034 ], "count": 3, "fragments": [ 2617, 1246, 498 ], "rebasePage": { "recognition": "G^TGCAC", "sitesOnPBR322": 3, "readOn": "2026-10-06", "agrees": true }, "nebcutter": null }, { "enzyme": "ApeKI", "plasmid": "L09137.2", "cuts": [ 42, 255, 328, 631, 712, 730, 1149, 1214, 1217, 1423, 1751, 2117 ], "count": 12, "fragments": [ 611, 419, 366, 328, 303, 213, 206, 81, 73, 65, 18, 3 ] }, { "enzyme": "ApeKI", "plasmid": "J01749.1", "cuts": [ 227, 616, 774, 1407, 1431, 1560, 1563, 1686, 2064, 2067, 2113, 2210, 2379, 2397, 2816, 2881, 2884, 3090, 3418, 3607, 3784 ], "count": 21, "fragments": [ 804, 633, 419, 389, 378, 328, 206, 189, 177, 169, 158, 129, 123, 97, 65, 46, 24, 18, 3, 3, 3 ] }, { "enzyme": "ApoI", "plasmid": "L09137.2", "cuts": [ 397 ], "count": 1, "fragments": [ 2686 ] }, { "enzyme": "ApoI", "plasmid": "J01749.1", "cuts": [ 4360 ], "count": 1, "fragments": [ 4361 ] }, { "enzyme": "AscI", "plasmid": "L09137.2", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "AscI", "plasmid": "J01749.1", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "AseI", "plasmid": "L09137.2", "cuts": [ 578, 637, 1872 ], "count": 3, "fragments": [ 1392, 1235, 59 ] }, { "enzyme": "AseI", "plasmid": "J01749.1", "cuts": [ 3539 ], "count": 1, "fragments": [ 4361 ] }, { "enzyme": "AsiSI", "plasmid": "L09137.2", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "AsiSI", "plasmid": "J01749.1", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "AvaI", "plasmid": "L09137.2", "cuts": [ 413 ], "count": 1, "fragments": [ 2686 ] }, { "enzyme": "AvaI", "plasmid": "J01749.1", "cuts": [ 1426 ], "count": 1, "fragments": [ 4361 ], "rebasePage": { "recognition": "C^YCGRG", "sitesOnPBR322": 1, "readOn": "2026-10-06", "agrees": true }, "nebcutter": null }, { "enzyme": "AvaII", "plasmid": "L09137.2", "cuts": [ 1838, 2060 ], "count": 2, "fragments": [ 2464, 222 ] }, { "enzyme": "AvaII", "plasmid": "J01749.1", "cuts": [ 800, 888, 1137, 1440, 1482, 1761, 3505, 3727 ], "count": 8, "fragments": [ 1744, 1434, 303, 279, 249, 222, 88, 42 ] }, { "enzyme": "AvrII", "plasmid": "L09137.2", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "AvrII", "plasmid": "J01749.1", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "BaeGI", "plasmid": "L09137.2", "cuts": [ 182, 1125, 2371 ], "count": 3, "fragments": [ 1246, 943, 497 ] }, { "enzyme": "BaeGI", "plasmid": "J01749.1", "cuts": [ 2294, 2792, 4038 ], "count": 3, "fragments": [ 2617, 1246, 498 ] }, { "enzyme": "BamHI", "plasmid": "L09137.2", "cuts": [ 418 ], "count": 1, "fragments": [ 2686 ] }, { "enzyme": "BamHI", "plasmid": "J01749.1", "cuts": [ 376 ], "count": 1, "fragments": [ 4361 ], "rebasePage": { "recognition": "G^GATCC", "sitesOnPBR322": 1, "readOn": "2026-10-06", "agrees": true }, "nebcutter": null }, { "enzyme": "BanI", "plasmid": "L09137.2", "cuts": [ 236, 409, 551, 1648 ], "count": 4, "fragments": [ 1274, 1097, 173, 142 ] }, { "enzyme": "BanI", "plasmid": "J01749.1", "cuts": [ 77, 120, 414, 435, 549, 767, 1206, 1290, 3315 ], "count": 9, "fragments": [ 2025, 1123, 439, 294, 218, 114, 84, 43, 21 ] }, { "enzyme": "BanII", "plasmid": "L09137.2", "cuts": [ 407 ], "count": 1, "fragments": [ 2686 ] }, { "enzyme": "BanII", "plasmid": "J01749.1", "cuts": [ 476, 490 ], "count": 2, "fragments": [ 4347, 14 ] }, { "enzyme": "BbsI", "plasmid": "L09137.2", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "BbsI", "plasmid": "J01749.1", "cuts": [ 731, 1594, 4345 ], "count": 3, "fragments": [ 2751, 863, 747 ], "rebasePage": { "recognition": "GAAGAC(2/6)", "sitesOnPBR322": 3, "readOn": "2026-10-06", "agrees": true }, "nebcutter": null }, { "enzyme": "BbvCI", "plasmid": "L09137.2", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "BbvCI", "plasmid": "J01749.1", "cuts": [], "count": 0, "fragments": [], "rebasePage": { "recognition": "CCTCAGC(-5/-2)", "sitesOnPBR322": 0, "readOn": "2026-10-06", "agrees": true }, "nebcutter": null }, { "enzyme": "BbvI", "plasmid": "L09137.2", "cuts": [ 54, 242, 315, 618, 699, 717, 1136, 1226, 1229, 1435, 1738, 2129 ], "count": 12, "fragments": [ 611, 419, 391, 303, 303, 206, 188, 90, 81, 73, 18, 3 ] }, { "enzyme": "BbvI", "plasmid": "J01749.1", "cuts": [ 214, 603, 786, 1419, 1443, 1547, 1550, 1673, 2054, 2076, 2125, 2222, 2366, 2384, 2803, 2893, 2896, 3102, 3405, 3594, 3796 ], "count": 21, "fragments": [ 779, 633, 419, 389, 381, 303, 206, 202, 189, 183, 144, 123, 104, 97, 90, 49, 24, 22, 18, 3, 3 ] }, { "enzyme": "BccI", "plasmid": "L09137.2", "cuts": [ 1744, 1868, 2155 ], "count": 3, "fragments": [ 2275, 287, 124 ] }, { "enzyme": "BccI", "plasmid": "J01749.1", "cuts": [ 453, 561, 983, 1087, 1394, 1406, 3411, 3535, 3822 ], "count": 9, "fragments": [ 2005, 992, 422, 307, 287, 124, 108, 104, 12 ] }, { "enzyme": "BceAI", 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"BglI", "plasmid": "J01749.1", "cuts": [ 936, 1170, 3487 ], "count": 3, "fragments": [ 2317, 1810, 234 ], "rebasePage": { "recognition": "GCCNNNN^NGGC", "sitesOnPBR322": 3, "readOn": "2026-10-06", "agrees": true }, "nebcutter": null }, { "enzyme": "BglII", "plasmid": "L09137.2", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "BglII", "plasmid": "J01749.1", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "BlpI", "plasmid": "L09137.2", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "BlpI", "plasmid": "J01749.1", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "BmgBI", "plasmid": "L09137.2", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "BmgBI", "plasmid": "J01749.1", "cuts": [], "count": 0, "fragments": [] }, { "enzyme": "BmrI", "plasmid": "L09137.2", "cuts": [ 360, 1740 ], "count": 2, "fragments": [ 1380, 1306 ] }, { "enzyme": "BmrI", "plasmid": "J01749.1", "cuts": [ 300, 621, 675, 2215, 3407 ], "count": 5, "fragments": [ 1540, 1254, 1192, 321, 54 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