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 | 5 - 82 | 6.5e-12 | RdRP1/2, RRM domain |
| PH_RDR2 | PF24823 | 101 - 232 | 3.8e-29 | RDR2 PH-like domain |
| RdRP_helical | PF26252 | 253 - 325 | 6e-11 | RNA dependent RNA polymerase, helical domain |
| RdRP | PF05183 | 352 - 926 | 2.7e-202 | RNA dependent RNA polymerase |
| RdRP_head | PF26253 | 952 - 1094 | 1.4e-43 | RdRP, head domain |
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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AanI | TTATAA | 1 cut(s) | 855 |
| Acc65I | GGTACC | 1 cut(s) | 3156 |
| AccB1I | GGYRCC | 3 cut(s) | 521, 710, 3156 |
| AccB7I | CCANNNNNTGG | 1 cut(s) | 2311 |
| AccI | GTMKAC | 3 cut(s) | 78, 426, 2643 |
| AccII | CGCG | 5 cut(s) | 481, 483, 698, 1341, 2160 |
| AccIII | TCCGGA | 2 cut(s) | 1084, 2704 |
| AciI | CCGC | 6 cut(s) | 1383, 2053, 2158, 2282, 2330, 3315 |
| AcoI | YGGCCR | 2 cut(s) | 205, 598 |
| AcsI | RAATTY | 8 cut(s) | 383, 799, 993, 1511, 1647, 2941, 3289, 3332 |
| AcuI | CTGAAG | 5 cut(s) | 123, 257, 1206, 2985, 2991 |
| AcyI | GRCGYC | 2 cut(s) | 2646, 3318 |
| AdeI | CACNNNGTG | 1 cut(s) | 2161 |
| AfaI | GTAC | 5 cut(s) | 968, 1733, 1778, 3158, 3283 |
| AfiI | CCNNNNNNNGG | 7 cut(s) | 128, 749, 761, 951, 2311, 2336, 2657 |
| AflIII | ACRYGT | 3 cut(s) | 2535, 2749, 3278 |
| AhdI | GACNNNNNGTC | 1 cut(s) | 3037 |
| AjnI | CCWGG | 5 cut(s) | 315, 978, 1458, 1475, 3083 |
| AjuI | GAANNNNNNNTTGG | 2 cut(s) | 2522, 2554 |
| AleI | CACNNNNGTG | 1 cut(s) | 3002 |
| Alw21I | GWGCWC | 4 cut(s) | 904, 1044, 1380, 1775 |
| Alw26I | GTCTC | 4 cut(s) | 103, 445, 1475, 2338 |
| Alw44I | GTGCAC | 2 cut(s) | 900, 1040 |
| AlwNI | CAGNNNCTG | 3 cut(s) | 101, 176, 1401 |
| Ama87I | CYCGRG | 1 cut(s) | 434 |
| Aor13HI | TCCGGA | 2 cut(s) | 1084, 2704 |
| AoxI | GGCC | 4 cut(s) | 205, 598, 1456, 1944 |
| ApaLI | GTGCAC | 2 cut(s) | 900, 1040 |
| ApeKI | GCWGC | 6 cut(s) | 301, 591, 933, 1916, 3137, 3192 |
| ApoI | RAATTY | 8 cut(s) | 383, 799, 993, 1511, 1647, 2941, 3289, 3332 |
| ArsI | GACNNNNNNTTYG | 2 cut(s) | 1289, 1321 |
| AseI | ATTAAT | 1 cut(s) | 3045 |
| Asp700I | GAANNNNTTC | 4 cut(s) | 1515, 1624, 2765, 3014 |
| Asp718I | GGTACC | 1 cut(s) | 3156 |
| AspLEI | GCGC | 3 cut(s) | 483, 700, 1341 |
| AspS9I | GGNCC | 4 cut(s) | 752, 1082, 1456, 3081 |
| AsuC2I | CCSGG | 3 cut(s) | 828, 1835, 2259 |
| AsuHPI | GGTGA | 9 cut(s) | 39, 574, 1307, 1372, 1801, 2147, 2296, 2788, 2821 |
| AsuII | TTCGAA | 1 cut(s) | 2552 |
| AvaI | CYCGRG | 1 cut(s) | 434 |
| AvaII | GGWCC | 3 cut(s) | 752, 1082, 3081 |
| AxyI | CCTNAGG | 1 cut(s) | 1125 |
| BaeGI | GKGCMC | 3 cut(s) | 526, 904, 1044 |
| BalI | TGGCCA | 1 cut(s) | 600 |
| BanI | GGYRCC | 3 cut(s) | 521, 710, 3156 |
| BanII | GRGCYC | 2 cut(s) | 230, 1380 |
| BarI | GAAGNNNNNNTAC | 4 cut(s) | 1612, 1644, 2964, 2996 |
| BbsI | GAAGAC | 2 cut(s) | 597, 2208 |
| Bbv12I | GWGCWC | 4 cut(s) | 904, 1044, 1380, 1775 |
| BbvCI | CCTCAGC | 1 cut(s) | 3224 |
| BbvI | GCAGC | 6 cut(s) | 288, 578, 920, 1928, 3149, 3179 |
| BceAI | ACGGC | 5 cut(s) | 192, 596, 2662, 2974, 3038 |
| BcgI | CGANNNNNNTGC | 2 cut(s) | 1031, 1065 |
| BciT130I | CCWGG | 5 cut(s) | 317, 980, 1460, 1477, 3085 |
| BciVI | GTATCC | 1 cut(s) | 1254 |
| BclI | TGATCA | 1 cut(s) | 3307 |
| BcnI | CCSGG | 3 cut(s) | 828, 1835, 2259 |
| BcoDI | GTCTC | 4 cut(s) | 103, 445, 1475, 2338 |
| BfaI | CTAG | 7 cut(s) | 243, 860, 870, 1245, 1449, 2238, 3078 |
| BfuI | GTATCC | 1 cut(s) | 1254 |
| BisI | GCNGC | 7 cut(s) | 302, 592, 934, 1917, 3138, 3193, 3316 |
| BlsI | GCNGC | 7 cut(s) | 303, 593, 935, 1918, 3139, 3194, 3317 |
| Bme1390I | CCNGG | 8 cut(s) | 317, 828, 980, 1460, 1477, 1835, 2259, 3085 |
| Bme18I | GGWCC | 3 cut(s) | 752, 1082, 3081 |
| BmeRI | GACNNNNNGTC | 1 cut(s) | 3037 |
| BmeT110I | CYCGRG | 1 cut(s) | 434 |
| BmgT120I | GGNCC | 4 cut(s) | 752, 1082, 1456, 3081 |
| BmiI | GGNNCC | 3 cut(s) | 523, 712, 3158 |
| BmrFI | CCNGG | 8 cut(s) | 317, 828, 980, 1460, 1477, 1835, 2259, 3085 |
| BmrI | ACTGGG | 2 cut(s) | 568, 3193 |
| BmsI | GCATC | 9 cut(s) | 152, 302, 1981, 2004, 2042, 2626, 2890, 2970, 3155 |
| BmuI | ACTGGG | 2 cut(s) | 568, 3193 |
| BpiI | GAAGAC | 2 cut(s) | 597, 2208 |
| BplI | GAGNNNNNCTC | 2 cut(s) | 428, 460 |
| BpmI | CTGGAG | 1 cut(s) | 92 |
| Bpu10I | CCTNAGC | 3 cut(s) | 491, 2365, 3224 |
| Bpu14I | TTCGAA | 1 cut(s) | 2552 |
| BpuEI | CTTGAG | 2 cut(s) | 1192, 1888 |
| BpuMI | CCSGG | 3 cut(s) | 828, 1835, 2259 |
| Bsa29I | ATCGAT | 1 cut(s) | 2895 |
| BsaAI | YACGTR | 5 cut(s) | 1776, 2690, 2736, 3168, 3281 |
| BsaHI | GRCGYC | 2 cut(s) | 2646, 3318 |
| BsaI | GGTCTC | 2 cut(s) | 445, 2338 |
| BsaJI | CCNNGG | 7 cut(s) | 527, 804, 827, 1476, 1825, 2832, 3233 |
| BsaWI | WCCGGW | 4 cut(s) | 83, 355, 1084, 2704 |
| BsaXI | ACNNNNNCTCC | 2 cut(s) | 1709, 1739 |
| Bsc4I | CCNNNNNNNGG | 7 cut(s) | 128, 749, 761, 951, 2311, 2336, 2657 |
| Bse118I | RCCGGY | 2 cut(s) | 2293, 2657 |
| Bse1I | ACTGG | 9 cut(s) | 511, 563, 601, 758, 909, 1406, 1884, 2176, 3188 |
| Bse21I | CCTNAGG | 1 cut(s) | 1125 |
| Bse3DI | GCAATG | 2 cut(s) | 2153, 2297 |
| BseAI | TCCGGA | 2 cut(s) | 1084, 2704 |
| BseBI | CCWGG | 5 cut(s) | 317, 980, 1460, 1477, 3085 |
| BseCI | ATCGAT | 1 cut(s) | 2895 |
| BseDI | CCNNGG | 7 cut(s) | 527, 804, 827, 1476, 1825, 2832, 3233 |
| BseLI | CCNNNNNNNGG | 7 cut(s) | 128, 749, 761, 951, 2311, 2336, 2657 |
| BseMI | GCAATG | 2 cut(s) | 2153, 2297 |
| BseMII | CTCAG | 6 cut(s) | 459, 1116, 1703, 2379, 2441, 3238 |
| BseNI | ACTGG | 9 cut(s) | 511, 563, 601, 758, 909, 1406, 1884, 2176, 3188 |
| BseRI | GAGGAG | 3 cut(s) | 433, 2385, 2510 |
| BseSI | GKGCMC | 3 cut(s) | 526, 904, 1044 |
| BseXI | GCAGC | 6 cut(s) | 288, 578, 920, 1928, 3149, 3179 |
| BseYI | CCCAGC | 1 cut(s) | 2935 |
| BsgI | GTGCAG | 3 cut(s) | 287, 1187, 3156 |
| Bsh1236I | CGCG | 5 cut(s) | 481, 483, 698, 1341, 2160 |
| Bsh1285I | CGRYCG | 1 cut(s) | 2441 |
| BshFI | GGCC | 4 cut(s) | 207, 600, 1458, 1946 |
| BshNI | GGYRCC | 3 cut(s) | 521, 710, 3156 |
| BshVI | ATCGAT | 1 cut(s) | 2895 |
| BsiEI | CGRYCG | 1 cut(s) | 2441 |
| BsiHKAI | GWGCWC | 4 cut(s) | 904, 1044, 1380, 1775 |
| BsiHKCI | CYCGRG | 1 cut(s) | 434 |
| BsiSI | CCGG | 9 cut(s) | 84, 356, 827, 1085, 1835, 2259, 2294, 2658, 2705 |
| BsiWI | CGTACG | 1 cut(s) | 3281 |
| BslFI | GGGAC | 6 cut(s) | 102, 391, 1424, 1817, 2420, 3284 |
| BslI | CCNNNNNNNGG | 7 cut(s) | 128, 749, 761, 951, 2311, 2336, 2657 |
| BsmAI | GTCTC | 4 cut(s) | 103, 445, 1475, 2338 |
| BsmFI | GGGAC | 6 cut(s) | 102, 391, 1424, 1817, 2420, 3284 |
| BsmI | GAATGC | 3 cut(s) | 1345, 2366, 2560 |
| BsnI | GGCC | 4 cut(s) | 207, 600, 1458, 1946 |
| Bso31I | GGTCTC | 2 cut(s) | 445, 2338 |
| BsoBI | CYCGRG | 1 cut(s) | 434 |
| Bsp119I | TTCGAA | 1 cut(s) | 2552 |
| Bsp1286I | GDGCHC | 6 cut(s) | 230, 526, 904, 1044, 1380, 1775 |
| Bsp13I | TCCGGA | 2 cut(s) | 1084, 2704 |
| BspACI | CCGC | 6 cut(s) | 1383, 2053, 2158, 2282, 2330, 3315 |
| BspANI | GGCC | 4 cut(s) | 207, 600, 1458, 1946 |
| BspCNI | CTCAG | 6 cut(s) | 458, 1117, 1704, 2378, 2440, 3237 |
| BspDI | ATCGAT | 1 cut(s) | 2895 |
| BspEI | TCCGGA | 2 cut(s) | 1084, 2704 |
| BspFNI | CGCG | 5 cut(s) | 481, 483, 698, 1341, 2160 |
| BspLI | GGNNCC | 3 cut(s) | 523, 712, 3158 |
| BspQI | GCTCTTC | 1 cut(s) | 1477 |
| BspT104I | TTCGAA | 1 cut(s) | 2552 |
| BspT107I | GGYRCC | 3 cut(s) | 521, 710, 3156 |
| BspTNI | GGTCTC | 2 cut(s) | 445, 2338 |
| BsrDI | GCAATG | 2 cut(s) | 2153, 2297 |
| BsrFI | RCCGGY | 2 cut(s) | 2293, 2657 |
| BsrI | ACTGG | 9 cut(s) | 511, 563, 601, 758, 909, 1406, 1884, 2176, 3188 |
| BssAI | RCCGGY | 2 cut(s) | 2293, 2657 |
| BssECI | CCNNGG | 7 cut(s) | 527, 804, 827, 1476, 1825, 2832, 3233 |
| BssNAI | GTATAC | 2 cut(s) | 79, 427 |
| BssNI | GRCGYC | 2 cut(s) | 2646, 3318 |
| BssT1I | CCWWGG | 3 cut(s) | 804, 1825, 2832 |
| Bst1107I | GTATAC | 2 cut(s) | 79, 427 |
| Bst2UI | CCWGG | 5 cut(s) | 317, 980, 1460, 1477, 3085 |
| Bst4CI | ACNGT | 4 cut(s) | 97, 915, 2030, 2566 |
| Bst6I | CTCTTC | 2 cut(s) | 1224, 1477 |
| BstACI | GRCGYC | 2 cut(s) | 2646, 3318 |
| BstAPI | GCANNNNNTGC | 1 cut(s) | 176 |
| BstBAI | YACGTR | 5 cut(s) | 1776, 2690, 2736, 3168, 3281 |
| BstBI | TTCGAA | 1 cut(s) | 2552 |
| BstDEI | CTNAG | 9 cut(s) | 445, 491, 1125, 1274, 1712, 2365, 2427, 2984, 3224 |
| BstDSI | CCRYGG | 1 cut(s) | 3233 |
| BstFNI | CGCG | 5 cut(s) | 481, 483, 698, 1341, 2160 |
| BstHHI | GCGC | 3 cut(s) | 483, 700, 1341 |
| BstMAI | GTCTC | 4 cut(s) | 103, 445, 1475, 2338 |
| BstMCI | CGRYCG | 1 cut(s) | 2441 |
| BstNI | CCWGG | 5 cut(s) | 317, 980, 1460, 1477, 3085 |
| BstNSI | RCATGY | 5 cut(s) | 933, 1726, 1969, 2539, 3346 |
| BstSCI | CCNGG | 8 cut(s) | 315, 826, 978, 1458, 1475, 1833, 2257, 3083 |
| BstSLI | GKGCMC | 3 cut(s) | 526, 904, 1044 |
| BstSNI | TACGTA | 2 cut(s) | 2736, 3168 |
| BstUI | CGCG | 5 cut(s) | 481, 483, 698, 1341, 2160 |
| BstV1I | GCAGC | 6 cut(s) | 288, 578, 920, 1928, 3149, 3179 |
| BstV2I | GAAGAC | 2 cut(s) | 597, 2208 |
| BstX2I | RGATCY | 1 cut(s) | 1129 |
| BstXI | CCANNNNNNTGG | 1 cut(s) | 518 |
| BstYI | RGATCY | 1 cut(s) | 1129 |
| BstZ17I | GTATAC | 2 cut(s) | 79, 427 |
| Bsu15I | ATCGAT | 1 cut(s) | 2895 |
| Bsu36I | CCTNAGG | 1 cut(s) | 1125 |
| BsuI | GTATCC | 1 cut(s) | 1254 |
| BsuRI | GGCC | 4 cut(s) | 207, 600, 1458, 1946 |
| BsuTUI | ATCGAT | 1 cut(s) | 2895 |
| BtgI | CCRYGG | 1 cut(s) | 3233 |
| BtsI | GCAGTG | 1 cut(s) | 63 |
| BtsIMutI | CAGTG | 8 cut(s) | 63, 765, 902, 1709, 2169, 3009, 3062, 3114 |
| CaiI | CAGNNNCTG | 3 cut(s) | 101, 176, 1401 |
| CfoI | GCGC | 3 cut(s) | 483, 700, 1341 |
| Cfr10I | RCCGGY | 2 cut(s) | 2293, 2657 |
| Cfr13I | GGNCC | 4 cut(s) | 752, 1082, 1456, 3081 |
| ClaI | ATCGAT | 1 cut(s) | 2895 |
| CseI | GACGC | 4 cut(s) | 699, 1353, 2654, 3307 |
| CsiI | ACCWGGT | 1 cut(s) | 3083 |
| Csp6I | GTAC | 5 cut(s) | 967, 1732, 1777, 3157, 3282 |
| CviQI | GTAC | 5 cut(s) | 967, 1732, 1777, 3157, 3282 |
| DdeI | CTNAG | 9 cut(s) | 445, 491, 1125, 1274, 1712, 2365, 2427, 2984, 3224 |
| DraIII | CACNNNGTG | 1 cut(s) | 2161 |
| DriI | GACNNNNNGTC | 1 cut(s) | 3037 |
| EaeI | YGGCCR | 2 cut(s) | 205, 598 |
| Eam1104I | CTCTTC | 2 cut(s) | 1224, 1477 |
| Eam1105I | GACNNNNNGTC | 1 cut(s) | 3037 |
| EarI | CTCTTC | 2 cut(s) | 1224, 1477 |
| Ecl136II | GAGCTC | 1 cut(s) | 1378 |
| Eco105I | TACGTA | 2 cut(s) | 2736, 3168 |
| Eco130I | CCWWGG | 3 cut(s) | 804, 1825, 2832 |
| Eco24I | GRGCYC | 2 cut(s) | 230, 1380 |
| Eco31I | GGTCTC | 2 cut(s) | 445, 2338 |
| Eco32I | GATATC | 1 cut(s) | 1581 |
| Eco47I | GGWCC | 3 cut(s) | 752, 1082, 3081 |
| Eco53kI | GAGCTC | 1 cut(s) | 1378 |
| Eco57I | CTGAAG | 5 cut(s) | 123, 257, 1206, 2985, 2991 |
| Eco81I | CCTNAGG | 1 cut(s) | 1125 |
| Eco88I | CYCGRG | 1 cut(s) | 434 |
| EcoICRI | GAGCTC | 1 cut(s) | 1378 |
| EcoO109I | RGGNCCY | 1 cut(s) | 3081 |
| EcoRI | GAATTC | 3 cut(s) | 993, 1511, 3289 |
| EcoRII | CCWGG | 5 cut(s) | 315, 978, 1458, 1475, 3083 |
| EcoRV | GATATC | 1 cut(s) | 1581 |
| EcoT14I | CCWWGG | 3 cut(s) | 804, 1825, 2832 |
| EcoT38I | GRGCYC | 2 cut(s) | 230, 1380 |
| ErhI | CCWWGG | 3 cut(s) | 804, 1825, 2832 |
| FalI | AAGNNNNNCTT | 2 cut(s) | 1852, 1884 |
| FaqI | GGGAC | 6 cut(s) | 102, 391, 1424, 1817, 2420, 3284 |
| FauI | CCCGC | 1 cut(s) | 2337 |
| FauNDI | CATATG | 1 cut(s) | 2307 |
| FbaI | TGATCA | 1 cut(s) | 3307 |
| FblI | GTMKAC | 3 cut(s) | 78, 426, 2643 |
| Fnu4HI | GCNGC | 7 cut(s) | 302, 592, 934, 1917, 3138, 3193, 3316 |
| FriOI | GRGCYC | 2 cut(s) | 230, 1380 |
| Fsp4HI | GCNGC | 7 cut(s) | 302, 592, 934, 1917, 3138, 3193, 3316 |
| FspBI | CTAG | 7 cut(s) | 243, 860, 870, 1245, 1449, 2238, 3078 |
| GlaI | GCGC | 3 cut(s) | 482, 699, 1340 |
| GluI | GCNGC | 7 cut(s) | 302, 592, 934, 1917, 3138, 3193, 3316 |
| GsaI | CCCAGC | 1 cut(s) | 2939 |
| GsuI | CTGGAG | 1 cut(s) | 92 |
| HaeIII | GGCC | 4 cut(s) | 207, 600, 1458, 1946 |
| HapII | CCGG | 9 cut(s) | 84, 356, 827, 1085, 1835, 2259, 2294, 2658, 2705 |
| HgaI | GACGC | 4 cut(s) | 699, 1353, 2654, 3307 |
| HhaI | GCGC | 3 cut(s) | 483, 700, 1341 |
| Hin1I | GRCGYC | 2 cut(s) | 2646, 3318 |
| Hin6I | GCGC | 3 cut(s) | 481, 698, 1339 |
| HinP1I | GCGC | 3 cut(s) | 481, 698, 1339 |
| HincII | GTYRAC | 4 cut(s) | 574, 1802, 2644, 2725 |
| HindII | GTYRAC | 4 cut(s) | 574, 1802, 2644, 2725 |
| HindIII | AAGCTT | 2 cut(s) | 543, 2762 |
| HpaII | CCGG | 9 cut(s) | 84, 356, 827, 1085, 1835, 2259, 2294, 2658, 2705 |
| HphI | GGTGA | 9 cut(s) | 39, 574, 1307, 1372, 1801, 2147, 2296, 2788, 2821 |
| Hpy99I | CGWCG | 4 cut(s) | 44, 213, 1760, 2648 |
| HpyAV | CCTTC | 9 cut(s) | 55, 83, 103, 232, 247, 680, 1877, 1954, 2584 |
| HpyCH4III | ACNGT | 4 cut(s) | 97, 915, 2030, 2566 |
| HpyCH4IV | ACGT | 9 cut(s) | 1758, 1775, 1953, 2289, 2689, 2735, 2749, 3167, 3280 |
| HpyF3I | CTNAG | 9 cut(s) | 445, 491, 1125, 1274, 1712, 2365, 2427, 2984, 3224 |
| HpySE526I | ACGT | 9 cut(s) | 1758, 1775, 1953, 2289, 2689, 2735, 2749, 3167, 3280 |
| Hsp92I | GRCGYC | 2 cut(s) | 2646, 3318 |
| HspAI | GCGC | 3 cut(s) | 481, 698, 1339 |
| Kpn2I | TCCGGA | 2 cut(s) | 1084, 2704 |
| KpnI | GGTACC | 1 cut(s) | 3160 |
| KroI | GCCGGC | 1 cut(s) | 2293 |
| KroNI | GCCGGC | 1 cut(s) | 2295 |
| Ksp22I | TGATCA | 1 cut(s) | 3307 |
| LguI | GCTCTTC | 1 cut(s) | 1477 |
| LmnI | GCTCC | 2 cut(s) | 466, 1770 |
| Lsp1109I | GCAGC | 6 cut(s) | 288, 578, 920, 1928, 3149, 3179 |
| LweI | GCATC | 9 cut(s) | 152, 302, 1981, 2004, 2042, 2626, 2890, 2970, 3155 |
| MabI | ACCWGGT | 1 cut(s) | 3083 |
| MaeI | CTAG | 7 cut(s) | 243, 860, 870, 1245, 1449, 2238, 3078 |
| MaeII | ACGT | 9 cut(s) | 1758, 1775, 1953, 2289, 2689, 2735, 2749, 3167, 3280 |
| MaeIII | GTNAC | 9 cut(s) | 45, 513, 1054, 1214, 1295, 1979, 2485, 3060, 3163 |
| MflI | RGATCY | 1 cut(s) | 1129 |
| MhlI | GDGCHC | 6 cut(s) | 230, 526, 904, 1044, 1380, 1775 |
| MlsI | TGGCCA | 1 cut(s) | 600 |
| MluNI | TGGCCA | 1 cut(s) | 600 |
| MlyI | GAGTC | 7 cut(s) | 53, 1010, 1062, 1839, 2402, 2516, 3047 |
| MmeI | TCCRAC | 3 cut(s) | 1764, 2794, 3270 |
| Mox20I | TGGCCA | 1 cut(s) | 600 |
| MroI | TCCGGA | 2 cut(s) | 1084, 2704 |
| MroNI | GCCGGC | 1 cut(s) | 2293 |
| MroXI | GAANNNNTTC | 4 cut(s) | 1515, 1624, 2765, 3014 |
| MscI | TGGCCA | 1 cut(s) | 600 |
| MseI | TTAA | 6 cut(s) | 6, 387, 846, 1488, 1892, 3045 |
| MslI | CAYNNNNRTG | 3 cut(s) | 819, 2355, 3002 |
| Msp20I | TGGCCA | 1 cut(s) | 600 |
| MspA1I | CMGCKG | 1 cut(s) | 2282 |
| MspI | CCGG | 9 cut(s) | 84, 356, 827, 1085, 1835, 2259, 2294, 2658, 2705 |
| MspR9I | CCNGG | 8 cut(s) | 317, 828, 980, 1460, 1477, 1835, 2259, 3085 |
| Mva1269I | GAATGC | 3 cut(s) | 1345, 2366, 2560 |
| MvaI | CCWGG | 5 cut(s) | 317, 980, 1460, 1477, 3085 |
| MvnI | CGCG | 5 cut(s) | 481, 483, 698, 1341, 2160 |
| NaeI | GCCGGC | 1 cut(s) | 2295 |
| NciI | CCSGG | 3 cut(s) | 828, 1835, 2259 |
| NdeI | CATATG | 1 cut(s) | 2307 |
| NgoMIV | GCCGGC | 1 cut(s) | 2293 |
| NlaIV | GGNNCC | 3 cut(s) | 523, 712, 3158 |
| NmuCI | GTSAC | 4 cut(s) | 45, 1054, 1295, 3060 |
| NspI | RCATGY | 5 cut(s) | 933, 1726, 1969, 2539, 3346 |
| NspV | TTCGAA | 1 cut(s) | 2552 |
| OliI | CACNNNNGTG | 1 cut(s) | 3002 |
| PaeI | GCATGC | 2 cut(s) | 933, 3346 |
| PaeR7I | CTCGAG | 1 cut(s) | 434 |
| PciI | ACATGT | 1 cut(s) | 2535 |
| PciSI | GCTCTTC | 1 cut(s) | 1477 |
| PcsI | WCGNNNNNNNCGW | 1 cut(s) | 1111 |
| PctI | GAATGC | 3 cut(s) | 1345, 2366, 2560 |
| PdiI | GCCGGC | 1 cut(s) | 2295 |
| PdmI | GAANNNNTTC | 4 cut(s) | 1515, 1624, 2765, 3014 |
| PfeI | GAWTC | 7 cut(s) | 16, 173, 416, 783, 1873, 2807, 3107 |
| Pfl23II | CGTACG | 1 cut(s) | 3281 |
| PflMI | CCANNNNNTGG | 1 cut(s) | 2311 |
| PfoI | TCCNGGA | 2 cut(s) | 1833, 2257 |
| PkrI | GCNGC | 7 cut(s) | 303, 593, 935, 1918, 3139, 3194, 3317 |
| PleI | GAGTC | 7 cut(s) | 52, 1009, 1061, 1838, 2402, 2515, 3046 |
| PpsI | GAGTC | 7 cut(s) | 52, 1009, 1061, 1838, 2402, 2515, 3046 |
| Ppu21I | YACGTR | 5 cut(s) | 1776, 2690, 2736, 3168, 3281 |
| PpuMI | RGGWCCY | 1 cut(s) | 3081 |
| PscI | ACATGT | 1 cut(s) | 2535 |
| PshBI | ATTAAT | 1 cut(s) | 3045 |
| PsiI | TTATAA | 1 cut(s) | 855 |
| Psp124BI | GAGCTC | 1 cut(s) | 1380 |
| Psp5II | RGGWCCY | 1 cut(s) | 3081 |
| Psp6I | CCWGG | 5 cut(s) | 315, 978, 1458, 1475, 3083 |
| PspFI | CCCAGC | 1 cut(s) | 2935 |
| PspGI | CCWGG | 5 cut(s) | 315, 978, 1458, 1475, 3083 |
| PspLI | CGTACG | 1 cut(s) | 3281 |
| PspN4I | GGNNCC | 3 cut(s) | 523, 712, 3158 |
| PspPI | GGNCC | 4 cut(s) | 752, 1082, 1456, 3081 |
| PspPPI | RGGWCCY | 1 cut(s) | 3081 |
| PspXI | VCTCGAGB | 1 cut(s) | 434 |
| PstNI | CAGNNNCTG | 3 cut(s) | 101, 176, 1401 |
| PsuI | RGATCY | 1 cut(s) | 1129 |
| RsaI | GTAC | 5 cut(s) | 968, 1733, 1778, 3158, 3283 |
| RsaNI | GTAC | 5 cut(s) | 967, 1732, 1777, 3157, 3282 |
| RseI | CAYNNNNRTG | 3 cut(s) | 819, 2355, 3002 |
| SacI | GAGCTC | 1 cut(s) | 1380 |
| SalI | GTCGAC | 1 cut(s) | 2642 |
| SapI | GCTCTTC | 1 cut(s) | 1477 |
| SaqAI | TTAA | 6 cut(s) | 6, 387, 846, 1488, 1892, 3045 |
| SatI | GCNGC | 7 cut(s) | 302, 592, 934, 1917, 3138, 3193, 3316 |
| Sau96I | GGNCC | 4 cut(s) | 752, 1082, 1456, 3081 |
| SchI | GAGTC | 7 cut(s) | 53, 1010, 1062, 1839, 2402, 2516, 3047 |
| ScrFI | CCNGG | 8 cut(s) | 317, 828, 980, 1460, 1477, 1835, 2259, 3085 |
| SduI | GDGCHC | 6 cut(s) | 230, 526, 904, 1044, 1380, 1775 |
| SexAI | ACCWGGT | 1 cut(s) | 3083 |
| SfaNI | GCATC | 9 cut(s) | 152, 302, 1981, 2004, 2042, 2626, 2890, 2970, 3155 |
| Sfr274I | CTCGAG | 1 cut(s) | 434 |
| SfuI | TTCGAA | 1 cut(s) | 2552 |
| SinI | GGWCC | 3 cut(s) | 752, 1082, 3081 |
| SlaI | CTCGAG | 1 cut(s) | 434 |
| SmiMI | CAYNNNNRTG | 3 cut(s) | 819, 2355, 3002 |
| SmlI | CTYRAG | 3 cut(s) | 434, 1171, 1903 |
| SmoI | CTYRAG | 3 cut(s) | 434, 1171, 1903 |
| SnaBI | TACGTA | 2 cut(s) | 2736, 3168 |
| SphI | GCATGC | 2 cut(s) | 933, 3346 |
| SsiI | CCGC | 6 cut(s) | 1383, 2053, 2158, 2282, 2330, 3315 |
| SspI | AATATT | 2 cut(s) | 1553, 1932 |
| SspMI | CTAG | 7 cut(s) | 243, 860, 870, 1245, 1449, 2238, 3078 |
| SstI | GAGCTC | 1 cut(s) | 1380 |
| StyD4I | CCNGG | 8 cut(s) | 315, 826, 978, 1458, 1475, 1833, 2257, 3083 |
| StyI | CCWWGG | 3 cut(s) | 804, 1825, 2832 |
| TaaI | ACNGT | 4 cut(s) | 97, 915, 2030, 2566 |
| TaiI | ACGT | 9 cut(s) | 1761, 1778, 1956, 2292, 2692, 2738, 2752, 3170, 3283 |
| TaqII | GACCGA | 1 cut(s) | 2455 |
| TatI | WGTACW | 1 cut(s) | 966 |
| TauI | GCSGC | 1 cut(s) | 3318 |
| TfiI | GAWTC | 7 cut(s) | 16, 173, 416, 783, 1873, 2807, 3107 |
| Tru1I | TTAA | 6 cut(s) | 6, 387, 846, 1488, 1892, 3045 |
| Tru9I | TTAA | 6 cut(s) | 6, 387, 846, 1488, 1892, 3045 |
| TscAI | CASTG | 8 cut(s) | 63, 765, 909, 1716, 2176, 3009, 3069, 3121 |
| TseFI | GTSAC | 4 cut(s) | 45, 1054, 1295, 3060 |
| TseI | GCWGC | 6 cut(s) | 301, 591, 933, 1916, 3137, 3192 |
| Tsp45I | GTSAC | 4 cut(s) | 45, 1054, 1295, 3060 |
| TspGWI | ACGGA | 4 cut(s) | 28, 618, 2060, 3222 |
| TspRI | CASTG | 8 cut(s) | 63, 765, 909, 1716, 2176, 3009, 3069, 3121 |
| Van91I | CCANNNNNTGG | 1 cut(s) | 2311 |
| VneI | GTGCAC | 2 cut(s) | 900, 1040 |
| VpaK11BI | GGWCC | 3 cut(s) | 752, 1082, 3081 |
| VspI | ATTAAT | 1 cut(s) | 3045 |
| XapI | RAATTY | 8 cut(s) | 383, 799, 993, 1511, 1647, 2941, 3289, 3332 |
| XceI | RCATGY | 5 cut(s) | 933, 1726, 1969, 2539, 3346 |
| XhoI | CTCGAG | 1 cut(s) | 434 |
| XmiI | GTMKAC | 3 cut(s) | 78, 426, 2643 |
| XmnI | GAANNNNTTC | 4 cut(s) | 1515, 1624, 2765, 3014 |
| XspI | CTAG | 7 cut(s) | 243, 860, 870, 1245, 1449, 2238, 3078 |