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 | 4 - 82 | 6.2e-12 | RdRP1/2, RRM domain |
| PH_RDR2 | PF24823 | 100 - 235 | 1.9e-32 | RDR2 PH-like domain |
| RdRP_helical | PF26252 | 253 - 328 | 4.5e-12 | RNA dependent RNA polymerase, helical domain |
| RdRP | PF05183 | 355 - 923 | 4.5e-197 | RNA dependent RNA polymerase |
| RdRP_head | PF26253 | 949 - 1097 | 3.7e-40 | RdRP, head domain |
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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AanI | TTATAA | 2 cut(s) | 534, 1980 |
| Acc36I | ACCTGC | 1 cut(s) | 1764 |
| Acc65I | GGTACC | 2 cut(s) | 1776, 3159 |
| AccB1I | GGYRCC | 4 cut(s) | 262, 518, 1776, 3159 |
| AccB7I | CCANNNNNTGG | 2 cut(s) | 125, 2302 |
| AccI | GTMKAC | 4 cut(s) | 77, 1080, 1820, 2674 |
| AccII | CGCG | 2 cut(s) | 1213, 2419 |
| AccIII | TCCGGA | 1 cut(s) | 731 |
| AciI | CCGC | 8 cut(s) | 1211, 1213, 1638, 1651, 2050, 2361, 2417, 2419 |
| AcsI | RAATTY | 7 cut(s) | 62, 155, 736, 808, 2064, 2197, 3001 |
| AcuI | CTGAAG | 4 cut(s) | 731, 1155, 2743, 2982 |
| AdeI | CACNNNGTG | 1 cut(s) | 2302 |
| AfaI | GTAC | 6 cut(s) | 977, 986, 1050, 1778, 2655, 3161 |
| AfiI | CCNNNNNNNGG | 8 cut(s) | 125, 662, 770, 1217, 1942, 2302, 2327, 2648 |
| AflII | CTTAAG | 1 cut(s) | 968 |
| AhdI | GACNNNNNGTC | 2 cut(s) | 2681, 3025 |
| AhlI | ACTAGT | 1 cut(s) | 2656 |
| AjnI | CCWGG | 6 cut(s) | 566, 912, 987, 1448, 1475, 1761 |
| AjuI | GAANNNNNNNTTGG | 6 cut(s) | 242, 274, 1541, 1573, 2513, 2545 |
| AloI | GAACNNNNNNTCC | 2 cut(s) | 1916, 1948 |
| Alw21I | GWGCWC | 3 cut(s) | 396, 438, 652 |
| Alw26I | GTCTC | 4 cut(s) | 48, 1392, 1475, 3210 |
| Alw44I | GTGCAC | 2 cut(s) | 392, 648 |
| Ama87I | CYCGRG | 3 cut(s) | 240, 836, 2248 |
| Aor13HI | TCCGGA | 1 cut(s) | 731 |
| AoxI | GGCC | 2 cut(s) | 1375, 2336 |
| ApaLI | GTGCAC | 2 cut(s) | 392, 648 |
| ApeKI | GCWGC | 6 cut(s) | 466, 942, 1433, 1445, 2172, 3140 |
| ApoI | RAATTY | 7 cut(s) | 62, 155, 736, 808, 2064, 2197, 3001 |
| ArsI | GACNNNNNNTTYG | 2 cut(s) | 1497, 1529 |
| Asp700I | GAANNNNTTC | 4 cut(s) | 1264, 1515, 1887, 2756 |
| Asp718I | GGTACC | 2 cut(s) | 1776, 3159 |
| AspA2I | CCTAGG | 2 cut(s) | 661, 769 |
| AspLEI | GCGC | 1 cut(s) | 131 |
| AspS9I | GGNCC | 2 cut(s) | 1091, 1375 |
| AsuC2I | CCSGG | 4 cut(s) | 837, 838, 2249, 2250 |
| AsuHPI | GGTGA | 6 cut(s) | 1005, 1307, 1421, 2144, 2779, 3107 |
| AsuII | TTCGAA | 1 cut(s) | 2874 |
| AvaI | CYCGRG | 3 cut(s) | 240, 836, 2248 |
| AvaII | GGWCC | 1 cut(s) | 1091 |
| AvrII | CCTAGG | 2 cut(s) | 661, 769 |
| BaeGI | GKGCMC | 4 cut(s) | 396, 523, 652, 913 |
| BamHI | GGATCC | 1 cut(s) | 874 |
| BanI | GGYRCC | 4 cut(s) | 262, 518, 1776, 3159 |
| BanII | GRGCYC | 1 cut(s) | 438 |
| BarI | GAAGNNNNNNTAC | 4 cut(s) | 1363, 1395, 2955, 2987 |
| BbsI | GAAGAC | 2 cut(s) | 719, 1041 |
| Bbv12I | GWGCWC | 3 cut(s) | 396, 438, 652 |
| BbvI | GCAGC | 6 cut(s) | 453, 929, 1445, 1457, 2184, 3152 |
| BciT130I | CCWGG | 6 cut(s) | 568, 914, 989, 1450, 1477, 1763 |
| BcnI | CCSGG | 4 cut(s) | 837, 838, 2249, 2250 |
| BcoDI | GTCTC | 4 cut(s) | 48, 1392, 1475, 3210 |
| BcuI | ACTAGT | 1 cut(s) | 2656 |
| BfmI | CTRYAG | 2 cut(s) | 165, 1197 |
| BfrI | CTTAAG | 1 cut(s) | 968 |
| BfuAI | ACCTGC | 1 cut(s) | 1764 |
| BglII | AGATCT | 1 cut(s) | 2084 |
| BisI | GCNGC | 8 cut(s) | 467, 943, 1434, 1446, 2173, 2362, 2420, 3141 |
| BlnI | CCTAGG | 2 cut(s) | 661, 769 |
| BlsI | GCNGC | 8 cut(s) | 468, 944, 1435, 1447, 2174, 2363, 2421, 3142 |
| Bme18I | GGWCC | 1 cut(s) | 1091 |
| BmeRI | GACNNNNNGTC | 2 cut(s) | 2681, 3025 |
| BmeT110I | CYCGRG | 3 cut(s) | 240, 836, 2248 |
| BmgT120I | GGNCC | 2 cut(s) | 1091, 1375 |
| BmiI | GGNNCC | 7 cut(s) | 264, 520, 762, 876, 1376, 1778, 3161 |
| BmrI | ACTGGG | 1 cut(s) | 3196 |
| BmuI | ACTGGG | 1 cut(s) | 3196 |
| BpiI | GAAGAC | 2 cut(s) | 719, 1041 |
| BpmI | CTGGAG | 3 cut(s) | 30, 89, 102 |
| Bpu10I | CCTNAGC | 1 cut(s) | 2356 |
| Bpu14I | TTCGAA | 1 cut(s) | 2874 |
| BpuEI | CTTGAG | 1 cut(s) | 452 |
| BpuMI | CCSGG | 4 cut(s) | 837, 838, 2249, 2250 |
| Bsa29I | ATCGAT | 1 cut(s) | 205 |
| BsaAI | YACGTR | 2 cut(s) | 515, 2672 |
| BsaI | GGTCTC | 1 cut(s) | 3210 |
| BsaWI | WCCGGW | 1 cut(s) | 731 |
| BsaXI | ACNNNNNCTCC | 2 cut(s) | 713, 743 |
| Bsc4I | CCNNNNNNNGG | 8 cut(s) | 125, 662, 770, 1217, 1942, 2302, 2327, 2648 |
| Bse1I | ACTGG | 6 cut(s) | 85, 508, 1406, 1926, 2653, 3191 |
| Bse3DI | GCAATG | 3 cut(s) | 1875, 2150, 2998 |
| BseAI | TCCGGA | 1 cut(s) | 731 |
| BseBI | CCWGG | 6 cut(s) | 568, 914, 989, 1450, 1477, 1763 |
| BseCI | ATCGAT | 1 cut(s) | 205 |
| BseGI | GGATG | 9 cut(s) | 314, 381, 504, 1362, 1410, 1634, 2102, 2284, 2341 |
| BseLI | CCNNNNNNNGG | 8 cut(s) | 125, 662, 770, 1217, 1942, 2302, 2327, 2648 |
| BseMI | GCAATG | 3 cut(s) | 1875, 2150, 2998 |
| BseMII | CTCAG | 5 cut(s) | 312, 1022, 2370, 2966, 3218 |
| BseNI | ACTGG | 6 cut(s) | 85, 508, 1406, 1926, 2653, 3191 |
| BseRI | GAGGAG | 5 cut(s) | 86, 338, 1247, 1252, 2510 |
| BseSI | GKGCMC | 4 cut(s) | 396, 523, 652, 913 |
| BseXI | GCAGC | 6 cut(s) | 453, 929, 1445, 1457, 2184, 3152 |
| BseYI | CCCAGC | 3 cut(s) | 2394, 2446, 2926 |
| BsgI | GTGCAG | 2 cut(s) | 1245, 1368 |
| Bsh1236I | CGCG | 2 cut(s) | 1213, 2419 |
| BshFI | GGCC | 2 cut(s) | 1377, 2338 |
| BshNI | GGYRCC | 4 cut(s) | 262, 518, 1776, 3159 |
| BshVI | ATCGAT | 1 cut(s) | 205 |
| BsiHKAI | GWGCWC | 3 cut(s) | 396, 438, 652 |
| BsiHKCI | CYCGRG | 3 cut(s) | 240, 836, 2248 |
| BsiSI | CCGG | 4 cut(s) | 457, 732, 837, 2249 |
| BslFI | GGGAC | 1 cut(s) | 2128 |
| BslI | CCNNNNNNNGG | 8 cut(s) | 125, 662, 770, 1217, 1942, 2302, 2327, 2648 |
| BsmAI | GTCTC | 4 cut(s) | 48, 1392, 1475, 3210 |
| BsmFI | GGGAC | 1 cut(s) | 2128 |
| BsmI | GAATGC | 1 cut(s) | 2357 |
| BsnI | GGCC | 2 cut(s) | 1377, 2338 |
| Bso31I | GGTCTC | 1 cut(s) | 3210 |
| BsoBI | CYCGRG | 3 cut(s) | 240, 836, 2248 |
| Bsp119I | TTCGAA | 1 cut(s) | 2874 |
| Bsp1286I | GDGCHC | 5 cut(s) | 396, 438, 523, 652, 913 |
| Bsp13I | TCCGGA | 1 cut(s) | 731 |
| Bsp1407I | TGTACA | 1 cut(s) | 1048 |
| Bsp19I | CCATGG | 2 cut(s) | 1936, 3236 |
| BspACI | CCGC | 8 cut(s) | 1211, 1213, 1638, 1651, 2050, 2361, 2417, 2419 |
| BspANI | GGCC | 2 cut(s) | 1377, 2338 |
| BspCNI | CTCAG | 5 cut(s) | 313, 1021, 2369, 2967, 3219 |
| BspDI | ATCGAT | 1 cut(s) | 205 |
| BspEI | TCCGGA | 1 cut(s) | 731 |
| BspFNI | CGCG | 2 cut(s) | 1213, 2419 |
| BspLI | GGNNCC | 7 cut(s) | 264, 520, 762, 876, 1376, 1778, 3161 |
| BspMAI | CTGCAG | 1 cut(s) | 169 |
| BspMI | ACCTGC | 1 cut(s) | 1764 |
| BspQI | GCTCTTC | 2 cut(s) | 1477, 2762 |
| BspT104I | TTCGAA | 1 cut(s) | 2874 |
| BspT107I | GGYRCC | 4 cut(s) | 262, 518, 1776, 3159 |
| BspTI | CTTAAG | 1 cut(s) | 968 |
| BspTNI | GGTCTC | 1 cut(s) | 3210 |
| BsrDI | GCAATG | 3 cut(s) | 1875, 2150, 2998 |
| BsrGI | TGTACA | 1 cut(s) | 1048 |
| BsrI | ACTGG | 6 cut(s) | 85, 508, 1406, 1926, 2653, 3191 |
| BssNAI | GTATAC | 2 cut(s) | 78, 1081 |
| BssT1I | CCWWGG | 5 cut(s) | 661, 769, 933, 1936, 3236 |
| Bst1107I | GTATAC | 2 cut(s) | 78, 1081 |
| Bst2UI | CCWGG | 6 cut(s) | 568, 914, 989, 1450, 1477, 1763 |
| Bst4CI | ACNGT | 7 cut(s) | 13, 37, 94, 702, 924, 2206, 2458 |
| Bst6I | CTCTTC | 4 cut(s) | 622, 1224, 1477, 2762 |
| BstAFI | CTTAAG | 1 cut(s) | 968 |
| BstAPI | GCANNNNNTGC | 1 cut(s) | 173 |
| BstAUI | TGTACA | 1 cut(s) | 1048 |
| BstBAI | YACGTR | 2 cut(s) | 515, 2672 |
| BstBI | TTCGAA | 1 cut(s) | 2874 |
| BstC8I | GCNNGC | 8 cut(s) | 843, 994, 998, 1660, 1707, 1866, 2188, 2286 |
| BstDEI | CTNAG | 7 cut(s) | 321, 1008, 1154, 1274, 2356, 2975, 3227 |
| BstDSI | CCRYGG | 4 cut(s) | 1211, 1936, 2417, 3236 |
| BstF5I | GGATG | 9 cut(s) | 314, 381, 504, 1362, 1410, 1634, 2102, 2284, 2341 |
| BstFNI | CGCG | 2 cut(s) | 1213, 2419 |
| BstHHI | GCGC | 1 cut(s) | 131 |
| BstMAI | GTCTC | 4 cut(s) | 48, 1392, 1475, 3210 |
| BstMWI | GCNNNNNNNGC | 7 cut(s) | 173, 970, 1442, 1659, 1916, 2361, 3146 |
| BstNI | CCWGG | 6 cut(s) | 568, 914, 989, 1450, 1477, 1763 |
| BstNSI | RCATGY | 3 cut(s) | 996, 1726, 3256 |
| BstSFI | CTRYAG | 2 cut(s) | 165, 1197 |
| BstSLI | GKGCMC | 4 cut(s) | 396, 523, 652, 913 |
| BstUI | CGCG | 2 cut(s) | 1213, 2419 |
| BstV1I | GCAGC | 6 cut(s) | 453, 929, 1445, 1457, 2184, 3152 |
| BstV2I | GAAGAC | 2 cut(s) | 719, 1041 |
| BstX2I | RGATCY | 2 cut(s) | 874, 2084 |
| BstXI | CCANNNNNNTGG | 1 cut(s) | 515 |
| BstYI | RGATCY | 2 cut(s) | 874, 2084 |
| BstZ17I | GTATAC | 2 cut(s) | 78, 1081 |
| Bsu15I | ATCGAT | 1 cut(s) | 205 |
| BsuRI | GGCC | 2 cut(s) | 1377, 2338 |
| BsuTUI | ATCGAT | 1 cut(s) | 205 |
| BtgI | CCRYGG | 4 cut(s) | 1211, 1936, 2417, 3236 |
| BtsCI | GGATG | 9 cut(s) | 314, 381, 504, 1362, 1410, 1634, 2102, 2284, 2341 |
| BtsI | GCAGTG | 1 cut(s) | 60 |
| BtsIMutI | CAGTG | 3 cut(s) | 33, 60, 1919 |
| BveI | ACCTGC | 1 cut(s) | 1764 |
| Cac8I | GCNNGC | 8 cut(s) | 843, 994, 998, 1660, 1707, 1866, 2188, 2286 |
| CfoI | GCGC | 1 cut(s) | 131 |
| Cfr13I | GGNCC | 2 cut(s) | 1091, 1375 |
| Cfr42I | CCGCGG | 2 cut(s) | 1214, 2420 |
| Cfr9I | CCCGGG | 2 cut(s) | 836, 2248 |
| ClaI | ATCGAT | 1 cut(s) | 205 |
| Csp6I | GTAC | 6 cut(s) | 976, 985, 1049, 1777, 2654, 3160 |
| CviQI | GTAC | 6 cut(s) | 976, 985, 1049, 1777, 2654, 3160 |
| DdeI | CTNAG | 7 cut(s) | 321, 1008, 1154, 1274, 2356, 2975, 3227 |
| DraI | TTTAAA | 1 cut(s) | 790 |
| DraIII | CACNNNGTG | 1 cut(s) | 2302 |
| DriI | GACNNNNNGTC | 2 cut(s) | 2681, 3025 |
| Eam1104I | CTCTTC | 4 cut(s) | 622, 1224, 1477, 2762 |
| Eam1105I | GACNNNNNGTC | 2 cut(s) | 2681, 3025 |
| EarI | CTCTTC | 4 cut(s) | 622, 1224, 1477, 2762 |
| EciI | GGCGGA | 1 cut(s) | 1627 |
| Ecl136II | GAGCTC | 1 cut(s) | 436 |
| Eco130I | CCWWGG | 5 cut(s) | 661, 769, 933, 1936, 3236 |
| Eco147I | AGGCCT | 1 cut(s) | 2338 |
| Eco24I | GRGCYC | 1 cut(s) | 438 |
| Eco31I | GGTCTC | 1 cut(s) | 3210 |
| Eco32I | GATATC | 2 cut(s) | 318, 1581 |
| Eco47I | GGWCC | 1 cut(s) | 1091 |
| Eco53kI | GAGCTC | 1 cut(s) | 436 |
| Eco57I | CTGAAG | 4 cut(s) | 731, 1155, 2743, 2982 |
| Eco88I | CYCGRG | 3 cut(s) | 240, 836, 2248 |
| EcoICRI | GAGCTC | 1 cut(s) | 436 |
| EcoO109I | RGGNCCY | 1 cut(s) | 1375 |
| EcoRI | GAATTC | 1 cut(s) | 155 |
| EcoRII | CCWGG | 6 cut(s) | 566, 912, 987, 1448, 1475, 1761 |
| EcoRV | GATATC | 2 cut(s) | 318, 1581 |
| EcoT14I | CCWWGG | 5 cut(s) | 661, 769, 933, 1936, 3236 |
| EcoT38I | GRGCYC | 1 cut(s) | 438 |
| ErhI | CCWWGG | 5 cut(s) | 661, 769, 933, 1936, 3236 |
| FalI | AAGNNNNNCTT | 2 cut(s) | 242, 274 |
| FaqI | GGGAC | 1 cut(s) | 2128 |
| FblI | GTMKAC | 4 cut(s) | 77, 1080, 1820, 2674 |
| Fnu4HI | GCNGC | 8 cut(s) | 467, 943, 1434, 1446, 2173, 2362, 2420, 3141 |
| FokI | GGATG | 9 cut(s) | 321, 388, 491, 1369, 1417, 1621, 2109, 2291, 2328 |
| FriOI | GRGCYC | 1 cut(s) | 438 |
| Fsp4HI | GCNGC | 8 cut(s) | 467, 943, 1434, 1446, 2173, 2362, 2420, 3141 |
| GlaI | GCGC | 1 cut(s) | 130 |
| GluI | GCNGC | 8 cut(s) | 467, 943, 1434, 1446, 2173, 2362, 2420, 3141 |
| GsaI | CCCAGC | 3 cut(s) | 2398, 2450, 2930 |
| GsuI | CTGGAG | 3 cut(s) | 30, 89, 102 |
| HaeIII | GGCC | 2 cut(s) | 1377, 2338 |
| HapII | CCGG | 4 cut(s) | 457, 732, 837, 2249 |
| HhaI | GCGC | 1 cut(s) | 131 |
| Hin6I | GCGC | 1 cut(s) | 129 |
| HinP1I | GCGC | 1 cut(s) | 129 |
| HindIII | AAGCTT | 1 cut(s) | 428 |
| HpaII | CCGG | 4 cut(s) | 457, 732, 837, 2249 |
| HphI | GGTGA | 6 cut(s) | 1005, 1307, 1421, 2144, 2779, 3107 |
| HpyAV | CCTTC | 7 cut(s) | 80, 1365, 1877, 2086, 2575, 2827, 3052 |
| HpyCH4III | ACNGT | 7 cut(s) | 13, 37, 94, 702, 924, 2206, 2458 |
| HpyCH4IV | ACGT | 2 cut(s) | 514, 2671 |
| HpyF10VI | GCNNNNNNNGC | 7 cut(s) | 173, 970, 1442, 1659, 1916, 2361, 3146 |
| HpyF3I | CTNAG | 7 cut(s) | 321, 1008, 1154, 1274, 2356, 2975, 3227 |
| HpySE526I | ACGT | 2 cut(s) | 514, 2671 |
| HspAI | GCGC | 1 cut(s) | 129 |
| Kpn2I | TCCGGA | 1 cut(s) | 731 |
| KpnI | GGTACC | 2 cut(s) | 1780, 3163 |
| KspI | CCGCGG | 2 cut(s) | 1214, 2420 |
| LguI | GCTCTTC | 2 cut(s) | 1477, 2762 |
| LmnI | GCTCC | 5 cut(s) | 441, 631, 766, 1770, 2622 |
| Lsp1109I | GCAGC | 6 cut(s) | 453, 929, 1445, 1457, 2184, 3152 |
| MaeII | ACGT | 2 cut(s) | 514, 2671 |
| MfeI | CAATTG | 3 cut(s) | 1334, 1802, 1877 |
| MflI | RGATCY | 2 cut(s) | 874, 2084 |
| MhlI | GDGCHC | 5 cut(s) | 396, 438, 523, 652, 913 |
| MlyI | GAGTC | 5 cut(s) | 50, 233, 2507, 2741, 3035 |
| MmeI | TCCRAC | 1 cut(s) | 1474 |
| MroI | TCCGGA | 1 cut(s) | 731 |
| MroXI | GAANNNNTTC | 4 cut(s) | 1264, 1515, 1887, 2756 |
| MseI | TTAA | 8 cut(s) | 641, 789, 927, 969, 1425, 2604, 2805, 3033 |
| MslI | CAYNNNNRTG | 3 cut(s) | 2346, 2625, 3154 |
| MspA1I | CMGCKG | 2 cut(s) | 1213, 2419 |
| MspCI | CTTAAG | 1 cut(s) | 968 |
| MspI | CCGG | 4 cut(s) | 457, 732, 837, 2249 |
| MunI | CAATTG | 3 cut(s) | 1334, 1802, 1877 |
| Mva1269I | GAATGC | 1 cut(s) | 2357 |
| MvaI | CCWGG | 6 cut(s) | 568, 914, 989, 1450, 1477, 1763 |
| MvnI | CGCG | 2 cut(s) | 1213, 2419 |
| MwoI | GCNNNNNNNGC | 7 cut(s) | 173, 970, 1442, 1659, 1916, 2361, 3146 |
| NciI | CCSGG | 4 cut(s) | 837, 838, 2249, 2250 |
| NcoI | CCATGG | 2 cut(s) | 1936, 3236 |
| NlaIV | GGNNCC | 7 cut(s) | 264, 520, 762, 876, 1376, 1778, 3161 |
| NmuCI | GTSAC | 6 cut(s) | 55, 292, 364, 1011, 1418, 2402 |
| NspI | RCATGY | 3 cut(s) | 996, 1726, 3256 |
| NspV | TTCGAA | 1 cut(s) | 2874 |
| PaeI | GCATGC | 1 cut(s) | 996 |
| PaeR7I | CTCGAG | 1 cut(s) | 240 |
| PceI | AGGCCT | 1 cut(s) | 2338 |
| PciSI | GCTCTTC | 2 cut(s) | 1477, 2762 |
| PcsI | WCGNNNNNNNCGW | 2 cut(s) | 1120, 2677 |
| PctI | GAATGC | 1 cut(s) | 2357 |
| PdmI | GAANNNNTTC | 4 cut(s) | 1264, 1515, 1887, 2756 |
| PfeI | GAWTC | 6 cut(s) | 1003, 1873, 1888, 2410, 2636, 2871 |
| PflMI | CCANNNNNTGG | 2 cut(s) | 125, 2302 |
| PkrI | GCNGC | 8 cut(s) | 468, 944, 1435, 1447, 2174, 2363, 2421, 3142 |
| PleI | GAGTC | 5 cut(s) | 49, 232, 2506, 2740, 3034 |
| PpsI | GAGTC | 5 cut(s) | 49, 232, 2506, 2740, 3034 |
| Ppu21I | YACGTR | 2 cut(s) | 515, 2672 |
| PsiI | TTATAA | 2 cut(s) | 534, 1980 |
| Psp124BI | GAGCTC | 1 cut(s) | 438 |
| Psp6I | CCWGG | 6 cut(s) | 566, 912, 987, 1448, 1475, 1761 |
| PspFI | CCCAGC | 3 cut(s) | 2394, 2446, 2926 |
| PspGI | CCWGG | 6 cut(s) | 566, 912, 987, 1448, 1475, 1761 |
| PspN4I | GGNNCC | 7 cut(s) | 264, 520, 762, 876, 1376, 1778, 3161 |
| PspPI | GGNCC | 2 cut(s) | 1091, 1375 |
| PsrI | GAACNNNNNNTAC | 2 cut(s) | 1041, 1073 |
| PstI | CTGCAG | 1 cut(s) | 169 |
| PsuI | RGATCY | 2 cut(s) | 874, 2084 |
| RsaI | GTAC | 6 cut(s) | 977, 986, 1050, 1778, 2655, 3161 |
| RsaNI | GTAC | 6 cut(s) | 976, 985, 1049, 1777, 2654, 3160 |
| RseI | CAYNNNNRTG | 3 cut(s) | 2346, 2625, 3154 |
| SacI | GAGCTC | 1 cut(s) | 438 |
| SacII | CCGCGG | 2 cut(s) | 1214, 2420 |
| SapI | GCTCTTC | 2 cut(s) | 1477, 2762 |
| SaqAI | TTAA | 8 cut(s) | 641, 789, 927, 969, 1425, 2604, 2805, 3033 |
| SatI | GCNGC | 8 cut(s) | 467, 943, 1434, 1446, 2173, 2362, 2420, 3141 |
| Sau96I | GGNCC | 2 cut(s) | 1091, 1375 |
| SchI | GAGTC | 5 cut(s) | 50, 233, 2507, 2741, 3035 |
| SduI | GDGCHC | 5 cut(s) | 396, 438, 523, 652, 913 |
| SfcI | CTRYAG | 2 cut(s) | 165, 1197 |
| Sfr274I | CTCGAG | 1 cut(s) | 240 |
| Sfr303I | CCGCGG | 2 cut(s) | 1214, 2420 |
| SfuI | TTCGAA | 1 cut(s) | 2874 |
| SgrBI | CCGCGG | 2 cut(s) | 1214, 2420 |
| SinI | GGWCC | 1 cut(s) | 1091 |
| SlaI | CTCGAG | 1 cut(s) | 240 |
| SmaI | CCCGGG | 2 cut(s) | 838, 2250 |
| SmiMI | CAYNNNNRTG | 3 cut(s) | 2346, 2625, 3154 |
| SmlI | CTYRAG | 3 cut(s) | 240, 431, 968 |
| SmoI | CTYRAG | 3 cut(s) | 240, 431, 968 |
| SpeI | ACTAGT | 1 cut(s) | 2656 |
| SphI | GCATGC | 1 cut(s) | 996 |
| SseBI | AGGCCT | 1 cut(s) | 2338 |
| SsiI | CCGC | 8 cut(s) | 1211, 1213, 1638, 1651, 2050, 2361, 2417, 2419 |
| SspI | AATATT | 2 cut(s) | 1553, 2879 |
| SstI | GAGCTC | 1 cut(s) | 438 |
| StuI | AGGCCT | 1 cut(s) | 2338 |
| StyI | CCWWGG | 5 cut(s) | 661, 769, 933, 1936, 3236 |
| TaaI | ACNGT | 7 cut(s) | 13, 37, 94, 702, 924, 2206, 2458 |
| TaiI | ACGT | 2 cut(s) | 517, 2674 |
| TaqI | TCGA | 5 cut(s) | 205, 241, 574, 2874, 3249 |
| TatI | WGTACW | 2 cut(s) | 1048, 2653 |
| TauI | GCSGC | 2 cut(s) | 2364, 2422 |
| TfiI | GAWTC | 6 cut(s) | 1003, 1873, 1888, 2410, 2636, 2871 |
| Tru1I | TTAA | 8 cut(s) | 641, 789, 927, 969, 1425, 2604, 2805, 3033 |
| Tru9I | TTAA | 8 cut(s) | 641, 789, 927, 969, 1425, 2604, 2805, 3033 |
| TscAI | CASTG | 3 cut(s) | 40, 60, 1926 |
| TseFI | GTSAC | 6 cut(s) | 55, 292, 364, 1011, 1418, 2402 |
| TseI | GCWGC | 6 cut(s) | 466, 942, 1433, 1445, 2172, 3140 |
| Tsp45I | GTSAC | 6 cut(s) | 55, 292, 364, 1011, 1418, 2402 |
| TspMI | CCCGGG | 2 cut(s) | 836, 2248 |
| TspRI | CASTG | 3 cut(s) | 40, 60, 1926 |
| Van91I | CCANNNNNTGG | 2 cut(s) | 125, 2302 |
| Vha464I | CTTAAG | 1 cut(s) | 968 |
| VneI | GTGCAC | 2 cut(s) | 392, 648 |
| VpaK11BI | GGWCC | 1 cut(s) | 1091 |
| XapI | RAATTY | 7 cut(s) | 62, 155, 736, 808, 2064, 2197, 3001 |
| XceI | RCATGY | 3 cut(s) | 996, 1726, 3256 |
| XhoI | CTCGAG | 1 cut(s) | 240 |
| XmaI | CCCGGG | 2 cut(s) | 836, 2248 |
| XmaJI | CCTAGG | 2 cut(s) | 661, 769 |
| XmiI | GTMKAC | 4 cut(s) | 77, 1080, 1820, 2674 |
| XmnI | GAANNNNTTC | 4 cut(s) | 1264, 1515, 1887, 2756 |