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 |
|---|---|---|---|---|
| PH_RDR2 | PF24823 | 55 - 190 | 1.8e-31 | RDR2 PH-like domain |
| RdRP_helical | PF26252 | 208 - 288 | 2.2e-09 | RNA dependent RNA polymerase, helical domain |
| RdRP | PF05183 | 307 - 876 | 9.5e-198 | RNA dependent RNA polymerase |
| RdRP_head | PF26253 | 900 - 1049 | 1.2e-40 | RdRP, head domain |
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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AanI | TTATAA | 2 cut(s) | 399, 729 |
| AatII | GACGTC | 1 cut(s) | 720 |
| Acc65I | GGTACC | 1 cut(s) | 3015 |
| AccB1I | GGYRCC | 3 cut(s) | 127, 383, 3015 |
| AccB7I | CCANNNNNTGG | 2 cut(s) | 2161, 2507 |
| AccBSI | CCGCTC | 1 cut(s) | 46 |
| AccI | GTMKAC | 1 cut(s) | 936 |
| AccII | CGCG | 1 cut(s) | 2278 |
| AclWI | GGATC | 9 cut(s) | 295, 734, 747, 1535, 1701, 1748, 2653, 2696, 2951 |
| AcsI | RAATTY | 5 cut(s) | 13, 673, 1201, 1445, 1920 |
| AcuI | CTGAAG | 4 cut(s) | 596, 1011, 1847, 2835 |
| AcvI | CACGTG | 1 cut(s) | 344 |
| AcyI | GRCGYC | 1 cut(s) | 717 |
| AdeI | CACNNNGTG | 1 cut(s) | 2161 |
| AfaI | GTAC | 4 cut(s) | 842, 1634, 2514, 3017 |
| AfiI | CCNNNNNNNGG | 5 cut(s) | 635, 2161, 2186, 2507, 2676 |
| AflIII | ACRYGT | 1 cut(s) | 837 |
| AhdI | GACNNNNNGTC | 2 cut(s) | 2540, 2881 |
| AhlI | ACTAGT | 1 cut(s) | 2515 |
| AjnI | CCWGG | 6 cut(s) | 777, 817, 1304, 1331, 1617, 2107 |
| AjuI | GAANNNNNNNTTGG | 4 cut(s) | 1397, 1429, 2372, 2404 |
| Alw21I | GWGCWC | 3 cut(s) | 137, 261, 517 |
| Alw26I | GTCTC | 4 cut(s) | 423, 1248, 1331, 3066 |
| Alw44I | GTGCAC | 2 cut(s) | 257, 513 |
| AlwI | GGATC | 9 cut(s) | 295, 734, 747, 1535, 1701, 1748, 2653, 2696, 2951 |
| Ama87I | CYCGRG | 1 cut(s) | 701 |
| AoxI | GGCC | 2 cut(s) | 1231, 2195 |
| ApaLI | GTGCAC | 2 cut(s) | 257, 513 |
| ApeKI | GCWGC | 6 cut(s) | 104, 115, 331, 465, 2220, 2996 |
| ApoI | RAATTY | 5 cut(s) | 13, 673, 1201, 1445, 1920 |
| ArsI | GACNNNNNNTTYG | 2 cut(s) | 1547, 1579 |
| AseI | ATTAAT | 1 cut(s) | 2739 |
| Asp700I | GAANNNNTTC | 3 cut(s) | 1371, 1743, 2615 |
| Asp718I | GGTACC | 1 cut(s) | 3015 |
| AspS9I | GGNCC | 3 cut(s) | 52, 947, 1231 |
| AsuC2I | CCSGG | 2 cut(s) | 702, 703 |
| AsuHPI | GGTGA | 7 cut(s) | 88, 861, 1163, 1277, 2000, 2273, 2833 |
| AsuII | TTCGAA | 2 cut(s) | 1590, 3105 |
| AvaI | CYCGRG | 1 cut(s) | 701 |
| AvaII | GGWCC | 2 cut(s) | 52, 947 |
| BaeGI | GKGCMC | 3 cut(s) | 261, 388, 517 |
| BaeI | ACNNNNGTAYC | 2 cut(s) | 2832, 2865 |
| BamHI | GGATCC | 1 cut(s) | 739 |
| BanI | GGYRCC | 3 cut(s) | 127, 383, 3015 |
| BanII | GRGCYC | 1 cut(s) | 137 |
| BarI | GAAGNNNNNNTAC | 6 cut(s) | 1219, 1251, 2808, 2840, 2910, 2942 |
| BbrPI | CACGTG | 1 cut(s) | 344 |
| Bbv12I | GWGCWC | 3 cut(s) | 137, 261, 517 |
| BbvI | GCAGC | 6 cut(s) | 116, 127, 318, 452, 2232, 3008 |
| BceAI | ACGGC | 1 cut(s) | 1837 |
| BcgI | CGANNNNNNTGC | 4 cut(s) | 1164, 1174, 1198, 1208 |
| BciT130I | CCWGG | 6 cut(s) | 779, 819, 1306, 1333, 1619, 2109 |
| BciVI | GTATCC | 2 cut(s) | 1110, 2919 |
| BcnI | CCSGG | 2 cut(s) | 702, 703 |
| BcoDI | GTCTC | 4 cut(s) | 423, 1248, 1331, 3066 |
| BcuI | ACTAGT | 1 cut(s) | 2515 |
| BfaI | CTAG | 6 cut(s) | 734, 747, 1172, 1958, 2516, 2676 |
| BfmI | CTRYAG | 1 cut(s) | 1053 |
| BfuI | GTATCC | 2 cut(s) | 1110, 2919 |
| BglII | AGATCT | 1 cut(s) | 1940 |
| Bme1390I | CCNGG | 8 cut(s) | 702, 703, 779, 819, 1306, 1333, 1619, 2109 |
| Bme18I | GGWCC | 2 cut(s) | 52, 947 |
| BmeRI | GACNNNNNGTC | 2 cut(s) | 2540, 2881 |
| BmeT110I | CYCGRG | 1 cut(s) | 701 |
| BmgT120I | GGNCC | 3 cut(s) | 52, 947, 1231 |
| BmiI | GGNNCC | 7 cut(s) | 129, 385, 627, 741, 1232, 1402, 3017 |
| BmrFI | CCNGG | 8 cut(s) | 702, 703, 779, 819, 1306, 1333, 1619, 2109 |
| BmrI | ACTGGG | 1 cut(s) | 3052 |
| BmsI | GCATC | 9 cut(s) | 30, 477, 1035, 1857, 1895, 2403, 2734, 3014, 3043 |
| BmuI | ACTGGG | 1 cut(s) | 3052 |
| BplI | GAGNNNNNCTC | 2 cut(s) | 290, 322 |
| BpmI | CTGGAG | 1 cut(s) | 2130 |
| Bpu10I | CCTNAGC | 1 cut(s) | 2215 |
| Bpu14I | TTCGAA | 2 cut(s) | 1590, 3105 |
| BpuEI | CTTGAG | 1 cut(s) | 317 |
| BpuMI | CCSGG | 2 cut(s) | 702, 703 |
| BsaAI | YACGTR | 2 cut(s) | 344, 380 |
| BsaHI | GRCGYC | 1 cut(s) | 717 |
| BsaI | GGTCTC | 1 cut(s) | 3066 |
| BsaXI | ACNNNNNCTCC | 6 cut(s) | 60, 90, 403, 433, 1087, 1117 |
| Bsc4I | CCNNNNNNNGG | 5 cut(s) | 635, 2161, 2186, 2507, 2676 |
| Bse118I | RCCGGY | 2 cut(s) | 2143, 2577 |
| Bse1I | ACTGG | 8 cut(s) | 373, 521, 1101, 1262, 2029, 2512, 3047, 3138 |
| Bse3DI | GCAATG | 2 cut(s) | 1731, 2006 |
| BseBI | CCWGG | 6 cut(s) | 779, 819, 1306, 1333, 1619, 2109 |
| BseLI | CCNNNNNNNGG | 5 cut(s) | 635, 2161, 2186, 2507, 2676 |
| BseMI | GCAATG | 2 cut(s) | 1731, 2006 |
| BseMII | CTCAG | 6 cut(s) | 177, 878, 1368, 2229, 2819, 3074 |
| BseNI | ACTGG | 8 cut(s) | 373, 521, 1101, 1262, 2029, 2512, 3047, 3138 |
| BseRI | GAGGAG | 4 cut(s) | 81, 203, 1721, 2369 |
| BseSI | GKGCMC | 3 cut(s) | 261, 388, 517 |
| BseXI | GCAGC | 6 cut(s) | 116, 127, 318, 452, 2232, 3008 |
| BseYI | CCCAGC | 3 cut(s) | 2253, 2305, 2779 |
| BsgI | GTGCAG | 2 cut(s) | 1101, 1224 |
| Bsh1236I | CGCG | 1 cut(s) | 2278 |
| BshFI | GGCC | 2 cut(s) | 1233, 2197 |
| BshNI | GGYRCC | 3 cut(s) | 127, 383, 3015 |
| BsiHKAI | GWGCWC | 3 cut(s) | 137, 261, 517 |
| BsiHKCI | CYCGRG | 1 cut(s) | 701 |
| BsiSI | CCGG | 5 cut(s) | 322, 597, 702, 2144, 2578 |
| BslFI | GGGAC | 1 cut(s) | 1984 |
| BslI | CCNNNNNNNGG | 5 cut(s) | 635, 2161, 2186, 2507, 2676 |
| BsmAI | GTCTC | 4 cut(s) | 423, 1248, 1331, 3066 |
| BsmFI | GGGAC | 1 cut(s) | 1984 |
| BsmI | GAATGC | 2 cut(s) | 2216, 2386 |
| BsnI | GGCC | 2 cut(s) | 1233, 2197 |
| Bso31I | GGTCTC | 1 cut(s) | 3066 |
| BsoBI | CYCGRG | 1 cut(s) | 701 |
| Bsp119I | TTCGAA | 2 cut(s) | 1590, 3105 |
| Bsp1286I | GDGCHC | 4 cut(s) | 137, 261, 388, 517 |
| Bsp1407I | TGTACA | 1 cut(s) | 840 |
| Bsp19I | CCATGG | 1 cut(s) | 3092 |
| BspANI | GGCC | 2 cut(s) | 1233, 2197 |
| BspCNI | CTCAG | 6 cut(s) | 178, 877, 1367, 2228, 2820, 3075 |
| BspFNI | CGCG | 1 cut(s) | 2278 |
| BspLI | GGNNCC | 7 cut(s) | 129, 385, 627, 741, 1232, 1402, 3017 |
| BspPI | GGATC | 9 cut(s) | 295, 734, 747, 1535, 1701, 1748, 2653, 2696, 2951 |
| BspT104I | TTCGAA | 2 cut(s) | 1590, 3105 |
| BspT107I | GGYRCC | 3 cut(s) | 127, 383, 3015 |
| BspTNI | GGTCTC | 1 cut(s) | 3066 |
| BsrBI | CCGCTC | 1 cut(s) | 46 |
| BsrDI | GCAATG | 2 cut(s) | 1731, 2006 |
| BsrFI | RCCGGY | 2 cut(s) | 2143, 2577 |
| BsrGI | TGTACA | 1 cut(s) | 840 |
| BsrI | ACTGG | 8 cut(s) | 373, 521, 1101, 1262, 2029, 2512, 3047, 3138 |
| BssAI | RCCGGY | 2 cut(s) | 2143, 2577 |
| BssNAI | GTATAC | 1 cut(s) | 937 |
| BssNI | GRCGYC | 1 cut(s) | 717 |
| BssT1I | CCWWGG | 4 cut(s) | 798, 1681, 2641, 3092 |
| Bst1107I | GTATAC | 1 cut(s) | 937 |
| Bst2UI | CCWGG | 6 cut(s) | 779, 819, 1306, 1333, 1619, 2109 |
| Bst6I | CTCTTC | 3 cut(s) | 487, 572, 1080 |
| BstACI | GRCGYC | 1 cut(s) | 717 |
| BstAPI | GCANNNNNTGC | 1 cut(s) | 2536 |
| BstAUI | TGTACA | 1 cut(s) | 840 |
| BstBAI | YACGTR | 2 cut(s) | 344, 380 |
| BstBI | TTCGAA | 2 cut(s) | 1590, 3105 |
| BstC8I | GCNNGC | 7 cut(s) | 94, 708, 850, 854, 2047, 2145, 2386 |
| BstDEI | CTNAG | 7 cut(s) | 186, 864, 1130, 1354, 2215, 2828, 3083 |
| BstDSI | CCRYGG | 2 cut(s) | 2276, 3092 |
| BstEII | GGTNACC | 1 cut(s) | 2261 |
| BstENI | CCTNNNNNAGG | 1 cut(s) | 2674 |
| BstFNI | CGCG | 1 cut(s) | 2278 |
| BstMAI | GTCTC | 4 cut(s) | 423, 1248, 1331, 3066 |
| BstMWI | GCNNNNNNNGC | 8 cut(s) | 1298, 1448, 1515, 1772, 2220, 2536, 2996, 3002 |
| BstNI | CCWGG | 6 cut(s) | 779, 819, 1306, 1333, 1619, 2109 |
| BstNSI | RCATGY | 4 cut(s) | 841, 852, 1582, 1813 |
| BstPI | GGTNACC | 1 cut(s) | 2261 |
| BstSCI | CCNGG | 8 cut(s) | 700, 701, 777, 817, 1304, 1331, 1617, 2107 |
| BstSFI | CTRYAG | 1 cut(s) | 1053 |
| BstSLI | GKGCMC | 3 cut(s) | 261, 388, 517 |
| BstUI | CGCG | 1 cut(s) | 2278 |
| BstV1I | GCAGC | 6 cut(s) | 116, 127, 318, 452, 2232, 3008 |
| BstX2I | RGATCY | 3 cut(s) | 300, 739, 1940 |
| BstXI | CCANNNNNNTGG | 1 cut(s) | 380 |
| BstYI | RGATCY | 3 cut(s) | 300, 739, 1940 |
| BstZ17I | GTATAC | 1 cut(s) | 937 |
| BsuI | GTATCC | 2 cut(s) | 1110, 2919 |
| BsuRI | GGCC | 2 cut(s) | 1233, 2197 |
| BtgI | CCRYGG | 2 cut(s) | 2276, 3092 |
| BtsI | GCAGTG | 2 cut(s) | 78, 103 |
| BtsIMutI | CAGTG | 6 cut(s) | 78, 88, 103, 1108, 1775, 2022 |
| Cac8I | GCNNGC | 7 cut(s) | 94, 708, 850, 854, 2047, 2145, 2386 |
| Cfr10I | RCCGGY | 2 cut(s) | 2143, 2577 |
| Cfr13I | GGNCC | 3 cut(s) | 52, 947, 1231 |
| Cfr42I | CCGCGG | 1 cut(s) | 2279 |
| Cfr9I | CCCGGG | 1 cut(s) | 701 |
| Csp6I | GTAC | 4 cut(s) | 841, 1633, 2513, 3016 |
| CviQI | GTAC | 4 cut(s) | 841, 1633, 2513, 3016 |
| DdeI | CTNAG | 7 cut(s) | 186, 864, 1130, 1354, 2215, 2828, 3083 |
| DraI | TTTAAA | 1 cut(s) | 1792 |
| DraIII | CACNNNGTG | 1 cut(s) | 2161 |
| DriI | GACNNNNNGTC | 2 cut(s) | 2540, 2881 |
| Eam1104I | CTCTTC | 3 cut(s) | 487, 572, 1080 |
| Eam1105I | GACNNNNNGTC | 2 cut(s) | 2540, 2881 |
| EarI | CTCTTC | 3 cut(s) | 487, 572, 1080 |
| EciI | GGCGGA | 3 cut(s) | 7, 164, 1413 |
| Ecl136II | GAGCTC | 1 cut(s) | 135 |
| Eco130I | CCWWGG | 4 cut(s) | 798, 1681, 2641, 3092 |
| Eco147I | AGGCCT | 1 cut(s) | 2197 |
| Eco24I | GRGCYC | 1 cut(s) | 137 |
| Eco31I | GGTCTC | 1 cut(s) | 3066 |
| Eco32I | GATATC | 4 cut(s) | 183, 997, 1437, 2980 |
| Eco47I | GGWCC | 2 cut(s) | 52, 947 |
| Eco53kI | GAGCTC | 1 cut(s) | 135 |
| Eco57I | CTGAAG | 4 cut(s) | 596, 1011, 1847, 2835 |
| Eco72I | CACGTG | 1 cut(s) | 344 |
| Eco88I | CYCGRG | 1 cut(s) | 701 |
| Eco91I | GGTNACC | 1 cut(s) | 2261 |
| EcoICRI | GAGCTC | 1 cut(s) | 135 |
| EcoNI | CCTNNNNNAGG | 1 cut(s) | 2674 |
| EcoO109I | RGGNCCY | 1 cut(s) | 1231 |
| EcoO65I | GGTNACC | 1 cut(s) | 2261 |
| EcoRI | GAATTC | 1 cut(s) | 1201 |
| EcoRII | CCWGG | 6 cut(s) | 777, 817, 1304, 1331, 1617, 2107 |
| EcoRV | GATATC | 4 cut(s) | 183, 997, 1437, 2980 |
| EcoT14I | CCWWGG | 4 cut(s) | 798, 1681, 2641, 3092 |
| EcoT38I | GRGCYC | 1 cut(s) | 137 |
| ErhI | CCWWGG | 4 cut(s) | 798, 1681, 2641, 3092 |
| FaqI | GGGAC | 1 cut(s) | 1984 |
| FblI | GTMKAC | 1 cut(s) | 936 |
| FriOI | GRGCYC | 1 cut(s) | 137 |
| FspBI | CTAG | 6 cut(s) | 734, 747, 1172, 1958, 2516, 2676 |
| GsaI | CCCAGC | 3 cut(s) | 2257, 2309, 2783 |
| GsuI | CTGGAG | 1 cut(s) | 2130 |
| HaeIII | GGCC | 2 cut(s) | 1233, 2197 |
| HapII | CCGG | 5 cut(s) | 322, 597, 702, 2144, 2578 |
| Hin1I | GRCGYC | 1 cut(s) | 717 |
| HincII | GTYRAC | 1 cut(s) | 1658 |
| HindII | GTYRAC | 1 cut(s) | 1658 |
| HindIII | AAGCTT | 2 cut(s) | 293, 2612 |
| HpaII | CCGG | 5 cut(s) | 322, 597, 702, 2144, 2578 |
| HphI | GGTGA | 7 cut(s) | 88, 861, 1163, 1277, 2000, 2273, 2833 |
| Hpy99I | CGWCG | 1 cut(s) | 1186 |
| HpyAV | CCTTC | 8 cut(s) | 536, 816, 884, 1221, 1733, 1765, 2434, 2680 |
| HpyCH4IV | ACGT | 3 cut(s) | 343, 379, 717 |
| HpyF10VI | GCNNNNNNNGC | 8 cut(s) | 1298, 1448, 1515, 1772, 2220, 2536, 2996, 3002 |
| HpyF3I | CTNAG | 7 cut(s) | 186, 864, 1130, 1354, 2215, 2828, 3083 |
| HpySE526I | ACGT | 3 cut(s) | 343, 379, 717 |
| Hsp92I | GRCGYC | 1 cut(s) | 717 |
| KpnI | GGTACC | 1 cut(s) | 3019 |
| KroI | GCCGGC | 1 cut(s) | 2143 |
| KroNI | GCCGGC | 1 cut(s) | 2145 |
| KspI | CCGCGG | 1 cut(s) | 2279 |
| LmnI | GCTCC | 5 cut(s) | 68, 496, 631, 1626, 2481 |
| Lsp1109I | GCAGC | 6 cut(s) | 116, 127, 318, 452, 2232, 3008 |
| LweI | GCATC | 9 cut(s) | 30, 477, 1035, 1857, 1895, 2403, 2734, 3014, 3043 |
| MaeI | CTAG | 6 cut(s) | 734, 747, 1172, 1958, 2516, 2676 |
| MaeII | ACGT | 3 cut(s) | 343, 379, 717 |
| MbiI | CCGCTC | 1 cut(s) | 46 |
| MflI | RGATCY | 3 cut(s) | 300, 739, 1940 |
| MhlI | GDGCHC | 4 cut(s) | 137, 261, 388, 517 |
| MlyI | GAGTC | 5 cut(s) | 13, 1195, 2366, 2600, 2891 |
| MmeI | TCCRAC | 2 cut(s) | 1568, 2644 |
| MroNI | GCCGGC | 1 cut(s) | 2143 |
| MroXI | GAANNNNTTC | 3 cut(s) | 1371, 1743, 2615 |
| MslI | CAYNNNNRTG | 4 cut(s) | 508, 2205, 2484, 3010 |
| MspA1I | CMGCKG | 2 cut(s) | 1735, 2278 |
| MspI | CCGG | 5 cut(s) | 322, 597, 702, 2144, 2578 |
| MspR9I | CCNGG | 8 cut(s) | 702, 703, 779, 819, 1306, 1333, 1619, 2109 |
| Mva1269I | GAATGC | 2 cut(s) | 2216, 2386 |
| MvaI | CCWGG | 6 cut(s) | 779, 819, 1306, 1333, 1619, 2109 |
| MvnI | CGCG | 1 cut(s) | 2278 |
| MwoI | GCNNNNNNNGC | 8 cut(s) | 1298, 1448, 1515, 1772, 2220, 2536, 2996, 3002 |
| NaeI | GCCGGC | 1 cut(s) | 2145 |
| NciI | CCSGG | 2 cut(s) | 702, 703 |
| NcoI | CCATGG | 1 cut(s) | 3092 |
| NgoMIV | GCCGGC | 1 cut(s) | 2143 |
| NlaIV | GGNNCC | 7 cut(s) | 129, 385, 627, 741, 1232, 1402, 3017 |
| NmeAIII | GCCGAG | 1 cut(s) | 2075 |
| NspI | RCATGY | 4 cut(s) | 841, 852, 1582, 1813 |
| NspV | TTCGAA | 2 cut(s) | 1590, 3105 |
| PaeI | GCATGC | 1 cut(s) | 852 |
| PceI | AGGCCT | 1 cut(s) | 2197 |
| PciI | ACATGT | 1 cut(s) | 837 |
| PcsI | WCGNNNNNNNCGW | 1 cut(s) | 976 |
| PctI | GAATGC | 2 cut(s) | 2216, 2386 |
| PdiI | GCCGGC | 1 cut(s) | 2145 |
| PdmI | GAANNNNTTC | 3 cut(s) | 1371, 1743, 2615 |
| PflMI | CCANNNNNTGG | 2 cut(s) | 2161, 2507 |
| PleI | GAGTC | 5 cut(s) | 12, 1194, 2365, 2599, 2890 |
| PmaCI | CACGTG | 1 cut(s) | 344 |
| PmlI | CACGTG | 1 cut(s) | 344 |
| PpsI | GAGTC | 5 cut(s) | 12, 1194, 2365, 2599, 2890 |
| Ppu21I | YACGTR | 2 cut(s) | 344, 380 |
| PscI | ACATGT | 1 cut(s) | 837 |
| PshBI | ATTAAT | 1 cut(s) | 2739 |
| PsiI | TTATAA | 2 cut(s) | 399, 729 |
| Psp124BI | GAGCTC | 1 cut(s) | 137 |
| Psp6I | CCWGG | 6 cut(s) | 777, 817, 1304, 1331, 1617, 2107 |
| PspCI | CACGTG | 1 cut(s) | 344 |
| PspEI | GGTNACC | 1 cut(s) | 2261 |
| PspFI | CCCAGC | 3 cut(s) | 2253, 2305, 2779 |
| PspGI | CCWGG | 6 cut(s) | 777, 817, 1304, 1331, 1617, 2107 |
| PspN4I | GGNNCC | 7 cut(s) | 129, 385, 627, 741, 1232, 1402, 3017 |
| PspPI | GGNCC | 3 cut(s) | 52, 947, 1231 |
| PsuI | RGATCY | 3 cut(s) | 300, 739, 1940 |
| PvuII | CAGCTG | 1 cut(s) | 1735 |
| RsaI | GTAC | 4 cut(s) | 842, 1634, 2514, 3017 |
| RsaNI | GTAC | 4 cut(s) | 841, 1633, 2513, 3016 |
| RseI | CAYNNNNRTG | 4 cut(s) | 508, 2205, 2484, 3010 |
| SacI | GAGCTC | 1 cut(s) | 137 |
| SacII | CCGCGG | 1 cut(s) | 2279 |
| Sau96I | GGNCC | 3 cut(s) | 52, 947, 1231 |
| SchI | GAGTC | 5 cut(s) | 13, 1195, 2366, 2600, 2891 |
| ScrFI | CCNGG | 8 cut(s) | 702, 703, 779, 819, 1306, 1333, 1619, 2109 |
| SduI | GDGCHC | 4 cut(s) | 137, 261, 388, 517 |
| SfaNI | GCATC | 9 cut(s) | 30, 477, 1035, 1857, 1895, 2403, 2734, 3014, 3043 |
| SfcI | CTRYAG | 1 cut(s) | 1053 |
| Sfr303I | CCGCGG | 1 cut(s) | 2279 |
| SfuI | TTCGAA | 2 cut(s) | 1590, 3105 |
| SgrBI | CCGCGG | 1 cut(s) | 2279 |
| SinI | GGWCC | 2 cut(s) | 52, 947 |
| SmaI | CCCGGG | 1 cut(s) | 703 |
| SmiMI | CAYNNNNRTG | 4 cut(s) | 508, 2205, 2484, 3010 |
| SmlI | CTYRAG | 1 cut(s) | 296 |
| SmoI | CTYRAG | 1 cut(s) | 296 |
| SpeI | ACTAGT | 1 cut(s) | 2515 |
| SphI | GCATGC | 1 cut(s) | 852 |
| SseBI | AGGCCT | 1 cut(s) | 2197 |
| SspI | AATATT | 1 cut(s) | 1409 |
| SspMI | CTAG | 6 cut(s) | 734, 747, 1172, 1958, 2516, 2676 |
| SstI | GAGCTC | 1 cut(s) | 137 |
| StuI | AGGCCT | 1 cut(s) | 2197 |
| StyD4I | CCNGG | 8 cut(s) | 700, 701, 777, 817, 1304, 1331, 1617, 2107 |
| StyI | CCWWGG | 4 cut(s) | 798, 1681, 2641, 3092 |
| TaiI | ACGT | 3 cut(s) | 346, 382, 720 |
| TaqI | TCGA | 9 cut(s) | 439, 999, 1184, 1539, 1590, 1918, 2885, 2937, 3105 |
| TatI | WGTACW | 2 cut(s) | 840, 2512 |
| TauI | GCSGC | 4 cut(s) | 23, 46, 2281, 2530 |
| TscAI | CASTG | 6 cut(s) | 78, 88, 103, 1108, 1782, 2029 |
| TseI | GCWGC | 6 cut(s) | 104, 115, 331, 465, 2220, 2996 |
| TspGWI | ACGGA | 1 cut(s) | 1437 |
| TspMI | CCCGGG | 1 cut(s) | 701 |
| TspRI | CASTG | 6 cut(s) | 78, 88, 103, 1108, 1782, 2029 |
| Van91I | CCANNNNNTGG | 2 cut(s) | 2161, 2507 |
| VneI | GTGCAC | 2 cut(s) | 257, 513 |
| VpaK11BI | GGWCC | 2 cut(s) | 52, 947 |
| VspI | ATTAAT | 1 cut(s) | 2739 |
| XagI | CCTNNNNNAGG | 1 cut(s) | 2674 |
| XapI | RAATTY | 5 cut(s) | 13, 673, 1201, 1445, 1920 |
| XbaI | TCTAGA | 1 cut(s) | 1957 |
| XceI | RCATGY | 4 cut(s) | 841, 852, 1582, 1813 |
| XmaI | CCCGGG | 1 cut(s) | 701 |
| XmiI | GTMKAC | 1 cut(s) | 936 |
| XmnI | GAANNNNTTC | 3 cut(s) | 1371, 1743, 2615 |
| XspI | CTAG | 6 cut(s) | 734, 747, 1172, 1958, 2516, 2676 |
| ZraI | GACGTC | 1 cut(s) | 718 |