Probably involved in the RNA silencing pathway and required for the generation of small interfering RNAs (siRNAs)
| Domain Name | Pfam ID | Position | E-value | Description |
|---|---|---|---|---|
| RRM_RdRP1_2 | PF26250 | 43 - 120 | 7.1e-13 | RdRP1/2, RRM domain |
| PH_RDR2 | PF24823 | 136 - 271 | 2.1e-32 | RDR2 PH-like domain |
| RdRP_helical | PF26252 | 289 - 365 | 1.3e-12 | RNA dependent RNA polymerase, helical domain |
| RdRP | PF05183 | 391 - 960 | 5.3e-200 | RNA dependent RNA polymerase |
| RdRP_head | PF26253 | 984 - 1129 | 8.4e-42 | RdRP, head domain |
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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AanI | TTATAA | 3 cut(s) | 642, 972, 2088 |
| Acc65I | GGTACC | 1 cut(s) | 3267 |
| AccB1I | GGYRCC | 3 cut(s) | 370, 626, 3267 |
| AccB7I | CCANNNNNTGG | 3 cut(s) | 233, 305, 2413 |
| AccBSI | CCGCTC | 1 cut(s) | 3084 |
| AccI | GTMKAC | 5 cut(s) | 185, 1158, 1188, 2552, 2745 |
| AccII | CGCG | 1 cut(s) | 1321 |
| AccIII | TCCGGA | 1 cut(s) | 839 |
| AciI | CCGC | 9 cut(s) | 161, 1108, 1300, 1319, 1321, 1650, 2384, 2780, 3084 |
| AcsI | RAATTY | 6 cut(s) | 170, 844, 916, 1453, 1697, 2172 |
| AcuI | CTGAAG | 3 cut(s) | 839, 1263, 3087 |
| AcvI | CACGTG | 1 cut(s) | 587 |
| AdeI | CACNNNGTG | 1 cut(s) | 2413 |
| AfaI | GTAC | 5 cut(s) | 326, 1085, 1094, 1886, 3269 |
| AflII | CTTAAG | 2 cut(s) | 748, 1076 |
| AhdI | GACNNNNNGTC | 1 cut(s) | 3133 |
| AhlI | ACTAGT | 1 cut(s) | 100 |
| AjnI | CCWGG | 4 cut(s) | 1556, 1583, 1869, 2359 |
| AjuI | GAANNNNNNNTTGG | 2 cut(s) | 1649, 1681 |
| AloI | GAACNNNNNNTCC | 4 cut(s) | 1016, 1048, 2024, 2056 |
| Alw21I | GWGCWC | 3 cut(s) | 504, 546, 760 |
| Alw26I | GTCTC | 5 cut(s) | 156, 1500, 1583, 2508, 3318 |
| Alw44I | GTGCAC | 2 cut(s) | 500, 756 |
| Ama87I | CYCGRG | 3 cut(s) | 348, 944, 2467 |
| Aor13HI | TCCGGA | 1 cut(s) | 839 |
| AoxI | GGCC | 4 cut(s) | 316, 1483, 2447, 2831 |
| ApaLI | GTGCAC | 2 cut(s) | 500, 756 |
| ApeKI | GCWGC | 6 cut(s) | 574, 708, 1050, 1124, 1553, 3248 |
| ApoI | RAATTY | 6 cut(s) | 170, 844, 916, 1453, 1697, 2172 |
| ArsI | GACNNNNNNTTYG | 2 cut(s) | 1799, 1831 |
| Asp700I | GAANNNNTTC | 3 cut(s) | 1623, 1995, 2867 |
| Asp718I | GGTACC | 1 cut(s) | 3267 |
| AspA2I | CCTAGG | 2 cut(s) | 769, 877 |
| AspS9I | GGNCC | 2 cut(s) | 1199, 1302 |
| AsuC2I | CCSGG | 3 cut(s) | 945, 946, 2221 |
| AsuHPI | GGTGA | 7 cut(s) | 73, 175, 1415, 1529, 2252, 2890, 3085 |
| AsuII | TTCGAA | 3 cut(s) | 1842, 2979, 3357 |
| AvaI | CYCGRG | 3 cut(s) | 348, 944, 2467 |
| AvaII | GGWCC | 2 cut(s) | 1199, 1302 |
| AvrII | CCTAGG | 2 cut(s) | 769, 877 |
| BaeGI | GKGCMC | 4 cut(s) | 504, 631, 760, 3181 |
| BaeI | ACNNNNGTAYC | 2 cut(s) | 3084, 3117 |
| BamHI | GGATCC | 1 cut(s) | 982 |
| BanI | GGYRCC | 3 cut(s) | 370, 626, 3267 |
| BanII | GRGCYC | 1 cut(s) | 546 |
| BarI | GAAGNNNNNNTAC | 4 cut(s) | 1056, 1088, 3060, 3092 |
| BauI | CACGAG | 1 cut(s) | 74 |
| BbrPI | CACGTG | 1 cut(s) | 587 |
| Bbv12I | GWGCWC | 3 cut(s) | 504, 546, 760 |
| BbvCI | CCTCAGC | 1 cut(s) | 2557 |
| BbvI | GCAGC | 6 cut(s) | 561, 695, 1037, 1136, 1565, 3260 |
| BceAI | ACGGC | 1 cut(s) | 2089 |
| BcgI | CGANNNNNNTGC | 4 cut(s) | 1416, 1426, 1450, 1460 |
| BciT130I | CCWGG | 4 cut(s) | 1558, 1585, 1871, 2361 |
| BciVI | GTATCC | 1 cut(s) | 1362 |
| BclI | TGATCA | 1 cut(s) | 589 |
| BcnI | CCSGG | 3 cut(s) | 945, 946, 2221 |
| BcoDI | GTCTC | 5 cut(s) | 156, 1500, 1583, 2508, 3318 |
| BcuI | ACTAGT | 1 cut(s) | 100 |
| BfmI | CTRYAG | 2 cut(s) | 273, 2528 |
| BfrI | CTTAAG | 2 cut(s) | 748, 1076 |
| BfuI | GTATCC | 1 cut(s) | 1362 |
| BglII | AGATCT | 1 cut(s) | 2192 |
| BisI | GCNGC | 7 cut(s) | 575, 709, 1051, 1125, 1554, 2780, 3249 |
| BlnI | CCTAGG | 2 cut(s) | 769, 877 |
| BlsI | GCNGC | 7 cut(s) | 576, 710, 1052, 1126, 1555, 2781, 3250 |
| Bme1390I | CCNGG | 7 cut(s) | 945, 946, 1558, 1585, 1871, 2221, 2361 |
| Bme18I | GGWCC | 2 cut(s) | 1199, 1302 |
| BmeRI | GACNNNNNGTC | 1 cut(s) | 3133 |
| BmeT110I | CYCGRG | 3 cut(s) | 348, 944, 2467 |
| BmgT120I | GGNCC | 2 cut(s) | 1199, 1302 |
| BmiI | GGNNCC | 7 cut(s) | 372, 628, 870, 984, 1654, 3195, 3269 |
| BmrFI | CCNGG | 7 cut(s) | 945, 946, 1558, 1585, 1871, 2221, 2361 |
| BmrI | ACTGGG | 2 cut(s) | 685, 3304 |
| BmsI | GCATC | 8 cut(s) | 407, 720, 1287, 2109, 2147, 2655, 2986, 3266 |
| BmuI | ACTGGG | 2 cut(s) | 685, 3304 |
| BpmI | CTGGAG | 3 cut(s) | 138, 197, 2382 |
| Bpu10I | CCTNAGC | 1 cut(s) | 2557 |
| Bpu14I | TTCGAA | 3 cut(s) | 1842, 2979, 3357 |
| BpuEI | CTTGAG | 1 cut(s) | 560 |
| BpuMI | CCSGG | 3 cut(s) | 945, 946, 2221 |
| BsaAI | YACGTR | 3 cut(s) | 14, 587, 623 |
| BsaI | GGTCTC | 2 cut(s) | 2508, 3318 |
| BsaWI | WCCGGW | 2 cut(s) | 188, 839 |
| BsaXI | ACNNNNNCTCC | 2 cut(s) | 821, 851 |
| Bse1I | ACTGG | 8 cut(s) | 48, 616, 680, 1514, 2034, 2281, 2764, 3299 |
| Bse3DI | GCAATG | 2 cut(s) | 1983, 2258 |
| BseAI | TCCGGA | 1 cut(s) | 839 |
| BseBI | CCWGG | 4 cut(s) | 1558, 1585, 1871, 2361 |
| BseGI | GGATG | 9 cut(s) | 422, 489, 612, 655, 1470, 1518, 2210, 2395, 2452 |
| BseMI | GCAATG | 2 cut(s) | 1983, 2258 |
| BseMII | CTCAG | 6 cut(s) | 420, 1130, 1373, 2559, 2571, 3071 |
| BseNI | ACTGG | 8 cut(s) | 48, 616, 680, 1514, 2034, 2281, 2764, 3299 |
| BseRI | GAGGAG | 6 cut(s) | 25, 194, 446, 1973, 2621, 3206 |
| BseSI | GKGCMC | 4 cut(s) | 504, 631, 760, 3181 |
| BseXI | GCAGC | 6 cut(s) | 561, 695, 1037, 1136, 1565, 3260 |
| BseYI | CCCAGC | 2 cut(s) | 2505, 3031 |
| BsgI | GTGCAG | 2 cut(s) | 1353, 1476 |
| Bsh1236I | CGCG | 1 cut(s) | 1321 |
| BshFI | GGCC | 4 cut(s) | 318, 1485, 2449, 2833 |
| BshNI | GGYRCC | 3 cut(s) | 370, 626, 3267 |
| BsiHKAI | GWGCWC | 3 cut(s) | 504, 546, 760 |
| BsiHKCI | CYCGRG | 3 cut(s) | 348, 944, 2467 |
| BsiSI | CCGG | 5 cut(s) | 189, 565, 840, 945, 2220 |
| BslFI | GGGAC | 1 cut(s) | 2236 |
| BsmAI | GTCTC | 5 cut(s) | 156, 1500, 1583, 2508, 3318 |
| BsmFI | GGGAC | 1 cut(s) | 2236 |
| BsmI | GAATGC | 1 cut(s) | 2468 |
| BsnI | GGCC | 4 cut(s) | 318, 1485, 2449, 2833 |
| Bso31I | GGTCTC | 2 cut(s) | 2508, 3318 |
| BsoBI | CYCGRG | 3 cut(s) | 348, 944, 2467 |
| Bsp119I | TTCGAA | 3 cut(s) | 1842, 2979, 3357 |
| Bsp1286I | GDGCHC | 5 cut(s) | 504, 546, 631, 760, 3181 |
| Bsp13I | TCCGGA | 1 cut(s) | 839 |
| Bsp19I | CCATGG | 1 cut(s) | 3344 |
| BspACI | CCGC | 9 cut(s) | 161, 1108, 1300, 1319, 1321, 1650, 2384, 2780, 3084 |
| BspANI | GGCC | 4 cut(s) | 318, 1485, 2449, 2833 |
| BspCNI | CTCAG | 6 cut(s) | 421, 1129, 1374, 2560, 2570, 3072 |
| BspEI | TCCGGA | 1 cut(s) | 839 |
| BspFNI | CGCG | 1 cut(s) | 1321 |
| BspHI | TCATGA | 1 cut(s) | 2581 |
| BspLI | GGNNCC | 7 cut(s) | 372, 628, 870, 984, 1654, 3195, 3269 |
| BspMAI | CTGCAG | 2 cut(s) | 277, 2532 |
| BspQI | GCTCTTC | 1 cut(s) | 1585 |
| BspT104I | TTCGAA | 3 cut(s) | 1842, 2979, 3357 |
| BspT107I | GGYRCC | 3 cut(s) | 370, 626, 3267 |
| BspTI | CTTAAG | 2 cut(s) | 748, 1076 |
| BspTNI | GGTCTC | 2 cut(s) | 2508, 3318 |
| BsrBI | CCGCTC | 1 cut(s) | 3084 |
| BsrDI | GCAATG | 2 cut(s) | 1983, 2258 |
| BsrI | ACTGG | 8 cut(s) | 48, 616, 680, 1514, 2034, 2281, 2764, 3299 |
| BssNAI | GTATAC | 4 cut(s) | 186, 1159, 1189, 2553 |
| BssSI | CACGAG | 1 cut(s) | 74 |
| BssT1I | CCWWGG | 7 cut(s) | 769, 877, 1020, 1041, 1933, 2044, 3344 |
| Bst1107I | GTATAC | 4 cut(s) | 186, 1159, 1189, 2553 |
| Bst2BI | CACGAG | 1 cut(s) | 74 |
| Bst2UI | CCWGG | 4 cut(s) | 1558, 1585, 1871, 2361 |
| Bst4CI | ACNGT | 9 cut(s) | 145, 202, 259, 810, 1032, 1600, 2317, 2639, 3183 |
| Bst6I | CTCTTC | 4 cut(s) | 730, 815, 1332, 1585 |
| BstAFI | CTTAAG | 2 cut(s) | 748, 1076 |
| BstAPI | GCANNNNNTGC | 1 cut(s) | 281 |
| BstBAI | YACGTR | 3 cut(s) | 14, 587, 623 |
| BstBI | TTCGAA | 3 cut(s) | 1842, 2979, 3357 |
| BstC8I | GCNNGC | 3 cut(s) | 951, 1102, 1106 |
| BstDEI | CTNAG | 7 cut(s) | 429, 1116, 1382, 2557, 2568, 3080, 3335 |
| BstDSI | CCRYGG | 2 cut(s) | 1319, 3344 |
| BstENI | CCTNNNNNAGG | 1 cut(s) | 2926 |
| BstF5I | GGATG | 9 cut(s) | 422, 489, 612, 655, 1470, 1518, 2210, 2395, 2452 |
| BstFNI | CGCG | 1 cut(s) | 1321 |
| BstMAI | GTCTC | 5 cut(s) | 156, 1500, 1583, 2508, 3318 |
| BstMWI | GCNNNNNNNGC | 7 cut(s) | 281, 1078, 1550, 1700, 2024, 2788, 3254 |
| BstNI | CCWGG | 4 cut(s) | 1558, 1585, 1871, 2361 |
| BstNSI | RCATGY | 3 cut(s) | 1104, 1157, 1834 |
| BstSCI | CCNGG | 7 cut(s) | 943, 944, 1556, 1583, 1869, 2219, 2359 |
| BstSFI | CTRYAG | 2 cut(s) | 273, 2528 |
| BstSLI | GKGCMC | 4 cut(s) | 504, 631, 760, 3181 |
| BstUI | CGCG | 1 cut(s) | 1321 |
| BstV1I | GCAGC | 6 cut(s) | 561, 695, 1037, 1136, 1565, 3260 |
| BstX2I | RGATCY | 2 cut(s) | 982, 2192 |
| BstXI | CCANNNNNNTGG | 1 cut(s) | 623 |
| BstYI | RGATCY | 2 cut(s) | 982, 2192 |
| BstZ17I | GTATAC | 4 cut(s) | 186, 1159, 1189, 2553 |
| BsuI | GTATCC | 1 cut(s) | 1362 |
| BsuRI | GGCC | 4 cut(s) | 318, 1485, 2449, 2833 |
| BtgI | CCRYGG | 2 cut(s) | 1319, 3344 |
| BtsCI | GGATG | 9 cut(s) | 422, 489, 612, 655, 1470, 1518, 2210, 2395, 2452 |
| BtsI | GCAGTG | 1 cut(s) | 2479 |
| BtsIMutI | CAGTG | 6 cut(s) | 55, 141, 673, 2027, 2274, 2479 |
| Cac8I | GCNNGC | 3 cut(s) | 951, 1102, 1106 |
| CciI | TCATGA | 1 cut(s) | 2581 |
| Cfr13I | GGNCC | 2 cut(s) | 1199, 1302 |
| Cfr42I | CCGCGG | 1 cut(s) | 1322 |
| Cfr9I | CCCGGG | 1 cut(s) | 944 |
| CpoI | CGGWCCG | 1 cut(s) | 1302 |
| Csp6I | GTAC | 5 cut(s) | 325, 1084, 1093, 1885, 3268 |
| CspI | CGGWCCG | 1 cut(s) | 1302 |
| CviQI | GTAC | 5 cut(s) | 325, 1084, 1093, 1885, 3268 |
| DdeI | CTNAG | 7 cut(s) | 429, 1116, 1382, 2557, 2568, 3080, 3335 |
| DraI | TTTAAA | 1 cut(s) | 2067 |
| DraIII | CACNNNGTG | 1 cut(s) | 2413 |
| DriI | GACNNNNNGTC | 1 cut(s) | 3133 |
| Eam1104I | CTCTTC | 4 cut(s) | 730, 815, 1332, 1585 |
| Eam1105I | GACNNNNNGTC | 1 cut(s) | 3133 |
| EarI | CTCTTC | 4 cut(s) | 730, 815, 1332, 1585 |
| EciI | GGCGGA | 1 cut(s) | 1665 |
| Ecl136II | GAGCTC | 1 cut(s) | 544 |
| Eco130I | CCWWGG | 7 cut(s) | 769, 877, 1020, 1041, 1933, 2044, 3344 |
| Eco147I | AGGCCT | 3 cut(s) | 318, 1485, 2449 |
| Eco24I | GRGCYC | 1 cut(s) | 546 |
| Eco31I | GGTCTC | 2 cut(s) | 2508, 3318 |
| Eco32I | GATATC | 5 cut(s) | 426, 1249, 1689, 2887, 3232 |
| Eco47I | GGWCC | 2 cut(s) | 1199, 1302 |
| Eco53kI | GAGCTC | 1 cut(s) | 544 |
| Eco57I | CTGAAG | 3 cut(s) | 839, 1263, 3087 |
| Eco72I | CACGTG | 1 cut(s) | 587 |
| Eco88I | CYCGRG | 3 cut(s) | 348, 944, 2467 |
| EcoICRI | GAGCTC | 1 cut(s) | 544 |
| EcoNI | CCTNNNNNAGG | 1 cut(s) | 2926 |
| EcoRI | GAATTC | 1 cut(s) | 1453 |
| EcoRII | CCWGG | 4 cut(s) | 1556, 1583, 1869, 2359 |
| EcoRV | GATATC | 5 cut(s) | 426, 1249, 1689, 2887, 3232 |
| EcoT14I | CCWWGG | 7 cut(s) | 769, 877, 1020, 1041, 1933, 2044, 3344 |
| EcoT38I | GRGCYC | 1 cut(s) | 546 |
| ErhI | CCWWGG | 7 cut(s) | 769, 877, 1020, 1041, 1933, 2044, 3344 |
| FaqI | GGGAC | 1 cut(s) | 2236 |
| FbaI | TGATCA | 1 cut(s) | 589 |
| FblI | GTMKAC | 5 cut(s) | 185, 1158, 1188, 2552, 2745 |
| Fnu4HI | GCNGC | 7 cut(s) | 575, 709, 1051, 1125, 1554, 2780, 3249 |
| FokI | GGATG | 9 cut(s) | 429, 496, 599, 662, 1477, 1525, 2217, 2402, 2439 |
| FriOI | GRGCYC | 1 cut(s) | 546 |
| Fsp4HI | GCNGC | 7 cut(s) | 575, 709, 1051, 1125, 1554, 2780, 3249 |
| GluI | GCNGC | 7 cut(s) | 575, 709, 1051, 1125, 1554, 2780, 3249 |
| GsaI | CCCAGC | 2 cut(s) | 2509, 3035 |
| GsuI | CTGGAG | 3 cut(s) | 138, 197, 2382 |
| HaeIII | GGCC | 4 cut(s) | 318, 1485, 2449, 2833 |
| HapII | CCGG | 5 cut(s) | 189, 565, 840, 945, 2220 |
| HincII | GTYRAC | 2 cut(s) | 1910, 2746 |
| HindII | GTYRAC | 2 cut(s) | 1910, 2746 |
| HindIII | AAGCTT | 2 cut(s) | 536, 2864 |
| HpaII | CCGG | 5 cut(s) | 189, 565, 840, 945, 2220 |
| HphI | GGTGA | 7 cut(s) | 73, 175, 1415, 1529, 2252, 2890, 3085 |
| Hpy99I | CGWCG | 2 cut(s) | 1438, 3291 |
| HpyAV | CCTTC | 9 cut(s) | 188, 640, 797, 1136, 1475, 1985, 2686, 2932, 3389 |
| HpyCH4III | ACNGT | 9 cut(s) | 145, 202, 259, 810, 1032, 1600, 2317, 2639, 3183 |
| HpyCH4IV | ACGT | 3 cut(s) | 13, 586, 622 |
| HpyF10VI | GCNNNNNNNGC | 7 cut(s) | 281, 1078, 1550, 1700, 2024, 2788, 3254 |
| HpyF3I | CTNAG | 7 cut(s) | 429, 1116, 1382, 2557, 2568, 3080, 3335 |
| HpySE526I | ACGT | 3 cut(s) | 13, 586, 622 |
| Kpn2I | TCCGGA | 1 cut(s) | 839 |
| KpnI | GGTACC | 1 cut(s) | 3271 |
| Ksp22I | TGATCA | 1 cut(s) | 589 |
| KspI | CCGCGG | 1 cut(s) | 1322 |
| LguI | GCTCTTC | 1 cut(s) | 1585 |
| LmnI | GCTCC | 7 cut(s) | 549, 739, 874, 1810, 1878, 2733, 3193 |
| Lsp1109I | GCAGC | 6 cut(s) | 561, 695, 1037, 1136, 1565, 3260 |
| LweI | GCATC | 8 cut(s) | 407, 720, 1287, 2109, 2147, 2655, 2986, 3266 |
| MaeII | ACGT | 3 cut(s) | 13, 586, 622 |
| MbiI | CCGCTC | 1 cut(s) | 3084 |
| MfeI | CAATTG | 1 cut(s) | 85 |
| MflI | RGATCY | 2 cut(s) | 982, 2192 |
| MhlI | GDGCHC | 5 cut(s) | 504, 546, 631, 760, 3181 |
| MlyI | GAGTC | 8 cut(s) | 26, 158, 341, 1447, 2618, 2741, 2852, 3143 |
| MmeI | TCCRAC | 3 cut(s) | 1582, 1820, 2896 |
| MroI | TCCGGA | 1 cut(s) | 839 |
| MroXI | GAANNNNTTC | 3 cut(s) | 1623, 1995, 2867 |
| MseI | TTAA | 9 cut(s) | 749, 1077, 1208, 1533, 1941, 2066, 2916, 3141, 3406 |
| MslI | CAYNNNNRTG | 3 cut(s) | 2457, 2736, 3262 |
| MspA1I | CMGCKG | 2 cut(s) | 1321, 1987 |
| MspCI | CTTAAG | 2 cut(s) | 748, 1076 |
| MspI | CCGG | 5 cut(s) | 189, 565, 840, 945, 2220 |
| MspR9I | CCNGG | 7 cut(s) | 945, 946, 1558, 1585, 1871, 2221, 2361 |
| MunI | CAATTG | 1 cut(s) | 85 |
| Mva1269I | GAATGC | 1 cut(s) | 2468 |
| MvaI | CCWGG | 4 cut(s) | 1558, 1585, 1871, 2361 |
| MvnI | CGCG | 1 cut(s) | 1321 |
| MwoI | GCNNNNNNNGC | 7 cut(s) | 281, 1078, 1550, 1700, 2024, 2788, 3254 |
| NciI | CCSGG | 3 cut(s) | 945, 946, 2221 |
| NcoI | CCATGG | 1 cut(s) | 3344 |
| NlaIV | GGNNCC | 7 cut(s) | 372, 628, 870, 984, 1654, 3195, 3269 |
| NmuCI | GTSAC | 7 cut(s) | 50, 163, 362, 400, 472, 1526, 2587 |
| NspI | RCATGY | 3 cut(s) | 1104, 1157, 1834 |
| NspV | TTCGAA | 3 cut(s) | 1842, 2979, 3357 |
| PaeI | GCATGC | 1 cut(s) | 1104 |
| PaeR7I | CTCGAG | 1 cut(s) | 348 |
| PagI | TCATGA | 1 cut(s) | 2581 |
| PceI | AGGCCT | 3 cut(s) | 318, 1485, 2449 |
| PciSI | GCTCTTC | 1 cut(s) | 1585 |
| PcsI | WCGNNNNNNNCGW | 1 cut(s) | 1228 |
| PctI | GAATGC | 1 cut(s) | 2468 |
| PdmI | GAANNNNTTC | 3 cut(s) | 1623, 1995, 2867 |
| PfeI | GAWTC | 6 cut(s) | 1111, 1844, 1981, 1996, 2521, 2976 |
| PflFI | GACNNNGTC | 1 cut(s) | 56 |
| PflMI | CCANNNNNTGG | 3 cut(s) | 233, 305, 2413 |
| PkrI | GCNGC | 7 cut(s) | 576, 710, 1052, 1126, 1555, 2781, 3250 |
| PleI | GAGTC | 8 cut(s) | 26, 157, 340, 1446, 2617, 2741, 2851, 3142 |
| PmaCI | CACGTG | 1 cut(s) | 587 |
| PmlI | CACGTG | 1 cut(s) | 587 |
| PpsI | GAGTC | 8 cut(s) | 26, 157, 340, 1446, 2617, 2741, 2851, 3142 |
| Ppu21I | YACGTR | 3 cut(s) | 14, 587, 623 |
| PsiI | TTATAA | 3 cut(s) | 642, 972, 2088 |
| Psp124BI | GAGCTC | 1 cut(s) | 546 |
| Psp6I | CCWGG | 4 cut(s) | 1556, 1583, 1869, 2359 |
| PspCI | CACGTG | 1 cut(s) | 587 |
| PspFI | CCCAGC | 2 cut(s) | 2505, 3031 |
| PspGI | CCWGG | 4 cut(s) | 1556, 1583, 1869, 2359 |
| PspN4I | GGNNCC | 7 cut(s) | 372, 628, 870, 984, 1654, 3195, 3269 |
| PspPI | GGNCC | 2 cut(s) | 1199, 1302 |
| PsrI | GAACNNNNNNTAC | 2 cut(s) | 1149, 1181 |
| PstI | CTGCAG | 2 cut(s) | 277, 2532 |
| PsuI | RGATCY | 2 cut(s) | 982, 2192 |
| PsyI | GACNNNGTC | 1 cut(s) | 56 |
| PvuII | CAGCTG | 1 cut(s) | 1987 |
| RsaI | GTAC | 5 cut(s) | 326, 1085, 1094, 1886, 3269 |
| RsaNI | GTAC | 5 cut(s) | 325, 1084, 1093, 1885, 3268 |
| RseI | CAYNNNNRTG | 3 cut(s) | 2457, 2736, 3262 |
| Rsr2I | CGGWCCG | 1 cut(s) | 1302 |
| RsrII | CGGWCCG | 1 cut(s) | 1302 |
| SacI | GAGCTC | 1 cut(s) | 546 |
| SacII | CCGCGG | 1 cut(s) | 1322 |
| SalI | GTCGAC | 1 cut(s) | 2744 |
| SapI | GCTCTTC | 1 cut(s) | 1585 |
| SaqAI | TTAA | 9 cut(s) | 749, 1077, 1208, 1533, 1941, 2066, 2916, 3141, 3406 |
| SatI | GCNGC | 7 cut(s) | 575, 709, 1051, 1125, 1554, 2780, 3249 |
| Sau96I | GGNCC | 2 cut(s) | 1199, 1302 |
| SchI | GAGTC | 8 cut(s) | 26, 158, 341, 1447, 2618, 2741, 2852, 3143 |
| ScrFI | CCNGG | 7 cut(s) | 945, 946, 1558, 1585, 1871, 2221, 2361 |
| SduI | GDGCHC | 5 cut(s) | 504, 546, 631, 760, 3181 |
| SfaNI | GCATC | 8 cut(s) | 407, 720, 1287, 2109, 2147, 2655, 2986, 3266 |
| SfcI | CTRYAG | 2 cut(s) | 273, 2528 |
| Sfr274I | CTCGAG | 1 cut(s) | 348 |
| Sfr303I | CCGCGG | 1 cut(s) | 1322 |
| SfuI | TTCGAA | 3 cut(s) | 1842, 2979, 3357 |
| SgrBI | CCGCGG | 1 cut(s) | 1322 |
| SinI | GGWCC | 2 cut(s) | 1199, 1302 |
| SlaI | CTCGAG | 1 cut(s) | 348 |
| SmaI | CCCGGG | 1 cut(s) | 946 |
| SmiMI | CAYNNNNRTG | 3 cut(s) | 2457, 2736, 3262 |
| SmlI | CTYRAG | 4 cut(s) | 348, 539, 748, 1076 |
| SmoI | CTYRAG | 4 cut(s) | 348, 539, 748, 1076 |
| SpeI | ACTAGT | 1 cut(s) | 100 |
| SphI | GCATGC | 1 cut(s) | 1104 |
| SseBI | AGGCCT | 3 cut(s) | 318, 1485, 2449 |
| SsiI | CCGC | 9 cut(s) | 161, 1108, 1300, 1319, 1321, 1650, 2384, 2780, 3084 |
| SspI | AATATT | 1 cut(s) | 1661 |
| SstI | GAGCTC | 1 cut(s) | 546 |
| StuI | AGGCCT | 3 cut(s) | 318, 1485, 2449 |
| StyD4I | CCNGG | 7 cut(s) | 943, 944, 1556, 1583, 1869, 2219, 2359 |
| StyI | CCWWGG | 7 cut(s) | 769, 877, 1020, 1041, 1933, 2044, 3344 |
| TaaI | ACNGT | 9 cut(s) | 145, 202, 259, 810, 1032, 1600, 2317, 2639, 3183 |
| TaiI | ACGT | 3 cut(s) | 16, 589, 625 |
| TatI | WGTACW | 2 cut(s) | 1083, 1092 |
| TauI | GCSGC | 1 cut(s) | 2782 |
| TfiI | GAWTC | 6 cut(s) | 1111, 1844, 1981, 1996, 2521, 2976 |
| Tru1I | TTAA | 9 cut(s) | 749, 1077, 1208, 1533, 1941, 2066, 2916, 3141, 3406 |
| Tru9I | TTAA | 9 cut(s) | 749, 1077, 1208, 1533, 1941, 2066, 2916, 3141, 3406 |
| TscAI | CASTG | 6 cut(s) | 55, 148, 680, 2034, 2281, 2479 |
| TseFI | GTSAC | 7 cut(s) | 50, 163, 362, 400, 472, 1526, 2587 |
| TseI | GCWGC | 6 cut(s) | 574, 708, 1050, 1124, 1553, 3248 |
| Tsp45I | GTSAC | 7 cut(s) | 50, 163, 362, 400, 472, 1526, 2587 |
| TspGWI | ACGGA | 5 cut(s) | 342, 505, 1294, 1689, 1748 |
| TspMI | CCCGGG | 1 cut(s) | 944 |
| TspRI | CASTG | 6 cut(s) | 55, 148, 680, 2034, 2281, 2479 |
| Tth111I | GACNNNGTC | 1 cut(s) | 56 |
| Van91I | CCANNNNNTGG | 3 cut(s) | 233, 305, 2413 |
| Vha464I | CTTAAG | 2 cut(s) | 748, 1076 |
| VneI | GTGCAC | 2 cut(s) | 500, 756 |
| VpaK11BI | GGWCC | 2 cut(s) | 1199, 1302 |
| XagI | CCTNNNNNAGG | 1 cut(s) | 2926 |
| XapI | RAATTY | 6 cut(s) | 170, 844, 916, 1453, 1697, 2172 |
| XbaI | TCTAGA | 1 cut(s) | 2209 |
| XceI | RCATGY | 3 cut(s) | 1104, 1157, 1834 |
| XhoI | CTCGAG | 1 cut(s) | 348 |
| XmaI | CCCGGG | 1 cut(s) | 944 |
| XmaJI | CCTAGG | 2 cut(s) | 769, 877 |
| XmiI | GTMKAC | 5 cut(s) | 185, 1158, 1188, 2552, 2745 |
| XmnI | GAANNNNTTC | 3 cut(s) | 1623, 1995, 2867 |