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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AciI | CCGC | 2 cut(s) | 54, 418 |
| AgsI | TTSAA | 3 cut(s) | 89, 123, 142 |
| AhlI | ACTAGT | 1 cut(s) | 196 |
| AluBI | AGCT | 5 cut(s) | 7, 170, 227, 242, 325 |
| AluI | AGCT | 5 cut(s) | 7, 170, 227, 242, 325 |
| Alw26I | GTCTC | 1 cut(s) | 317 |
| AoxI | GGCC | 1 cut(s) | 29 |
| AspS9I | GGNCC | 1 cut(s) | 30 |
| AsuNHI | GCTAGC | 1 cut(s) | 22 |
| BaeI | ACNNNNGTAYC | 2 cut(s) | 84, 117 |
| BbsI | GAAGAC | 1 cut(s) | 108 |
| BccI | CCATC | 1 cut(s) | 310 |
| BcoDI | GTCTC | 1 cut(s) | 317 |
| BcuI | ACTAGT | 1 cut(s) | 196 |
| BfaI | CTAG | 3 cut(s) | 23, 197, 263 |
| BlpI | GCTNAGC | 1 cut(s) | 321 |
| BmgT120I | GGNCC | 1 cut(s) | 30 |
| BmtI | GCTAGC | 1 cut(s) | 26 |
| BpiI | GAAGAC | 1 cut(s) | 108 |
| BplI | GAGNNNNNCTC | 2 cut(s) | 57, 89 |
| BpmI | CTGGAG | 1 cut(s) | 156 |
| Bpu1102I | GCTNAGC | 1 cut(s) | 321 |
| Bse3DI | GCAATG | 1 cut(s) | 315 |
| BseGI | GGATG | 1 cut(s) | 302 |
| BseMI | GCAATG | 1 cut(s) | 315 |
| BseMII | CTCAG | 1 cut(s) | 335 |
| BshFI | GGCC | 1 cut(s) | 31 |
| BsmAI | GTCTC | 1 cut(s) | 317 |
| BsnI | GGCC | 1 cut(s) | 31 |
| Bsp143I | GATC | 1 cut(s) | 175 |
| Bsp1720I | GCTNAGC | 1 cut(s) | 321 |
| BspACI | CCGC | 2 cut(s) | 54, 418 |
| BspANI | GGCC | 1 cut(s) | 31 |
| BspCNI | CTCAG | 1 cut(s) | 334 |
| BspOI | GCTAGC | 1 cut(s) | 26 |
| BsrDI | GCAATG | 1 cut(s) | 315 |
| BssMI | GATC | 1 cut(s) | 175 |
| Bst4CI | ACNGT | 1 cut(s) | 97 |
| BstC8I | GCNNGC | 1 cut(s) | 24 |
| BstDEI | CTNAG | 2 cut(s) | 17, 321 |
| BstF5I | GGATG | 1 cut(s) | 302 |
| BstKTI | GATC | 1 cut(s) | 178 |
| BstMAI | GTCTC | 1 cut(s) | 317 |
| BstMBI | GATC | 1 cut(s) | 175 |
| BstMWI | GCNNNNNNNGC | 1 cut(s) | 28 |
| BstNSI | RCATGY | 1 cut(s) | 415 |
| BstV2I | GAAGAC | 1 cut(s) | 108 |
| BsuRI | GGCC | 1 cut(s) | 31 |
| BtsCI | GGATG | 1 cut(s) | 302 |
| Cac8I | GCNNGC | 1 cut(s) | 24 |
| Cfr13I | GGNCC | 1 cut(s) | 30 |
| CviAII | CATG | 3 cut(s) | 27, 383, 412 |
| DdeI | CTNAG | 2 cut(s) | 17, 321 |
| DpnI | GATC | 1 cut(s) | 177 |
| DpnII | GATC | 1 cut(s) | 175 |
| DraI | TTTAAA | 1 cut(s) | 234 |
| EciI | GGCGGA | 1 cut(s) | 407 |
| FaeI | CATG | 3 cut(s) | 30, 386, 415 |
| FaiI | YATR | 6 cut(s) | 28, 329, 339, 384, 413, 425 |
| FatI | CATG | 3 cut(s) | 26, 382, 411 |
| FokI | GGATG | 1 cut(s) | 289 |
| FspBI | CTAG | 3 cut(s) | 23, 197, 263 |
| GsuI | CTGGAG | 1 cut(s) | 156 |
| HaeIII | GGCC | 1 cut(s) | 31 |
| Hin1II | CATG | 3 cut(s) | 30, 386, 415 |
| HindIII | AAGCTT | 2 cut(s) | 5, 225 |
| Hpy188I | TCNGA | 3 cut(s) | 280, 295, 390 |
| Hpy188III | TCNNGA | 1 cut(s) | 173 |
| HpyCH4III | ACNGT | 1 cut(s) | 97 |
| HpyCH4IV | ACGT | 1 cut(s) | 275 |
| HpyF10VI | GCNNNNNNNGC | 1 cut(s) | 28 |
| HpyF3I | CTNAG | 2 cut(s) | 17, 321 |
| HpySE526I | ACGT | 1 cut(s) | 275 |
| Hsp92II | CATG | 3 cut(s) | 30, 386, 415 |
| Kzo9I | GATC | 1 cut(s) | 175 |
| LmnI | GCTCC | 2 cut(s) | 175, 420 |
| LpnPI | CCDG | 2 cut(s) | 61, 186 |
| MaeI | CTAG | 3 cut(s) | 23, 197, 263 |
| MaeII | ACGT | 1 cut(s) | 275 |
| MaeIII | GTNAC | 1 cut(s) | 56 |
| MalI | GATC | 1 cut(s) | 177 |
| MboI | GATC | 1 cut(s) | 175 |
| MboII | GAAGA | 4 cut(s) | 101, 108, 111, 342 |
| MluCI | AATT | 3 cut(s) | 251, 296, 426 |
| MseI | TTAA | 2 cut(s) | 233, 429 |
| MwoI | GCNNNNNNNGC | 1 cut(s) | 28 |
| NdeII | GATC | 1 cut(s) | 175 |
| NheI | GCTAGC | 1 cut(s) | 22 |
| NlaIII | CATG | 3 cut(s) | 30, 386, 415 |
| NmuCI | GTSAC | 1 cut(s) | 56 |
| NspI | RCATGY | 1 cut(s) | 415 |
| PspPI | GGNCC | 1 cut(s) | 30 |
| SaqAI | TTAA | 2 cut(s) | 233, 429 |
| Sau3AI | GATC | 1 cut(s) | 175 |
| Sau96I | GGNCC | 1 cut(s) | 30 |
| SetI | ASST | 9 cut(s) | 9, 50, 84, 172, 229, 244, 264, 278, 327 |
| SpeI | ACTAGT | 1 cut(s) | 196 |
| Sse9I | AATT | 3 cut(s) | 251, 296, 426 |
| SsiI | CCGC | 2 cut(s) | 54, 418 |
| SspI | AATATT | 1 cut(s) | 145 |
| SspMI | CTAG | 3 cut(s) | 23, 197, 263 |
| TaaI | ACNGT | 1 cut(s) | 97 |
| TaiI | ACGT | 1 cut(s) | 278 |
| TaqI | TCGA | 2 cut(s) | 75, 257 |
| TasI | AATT | 3 cut(s) | 251, 296, 426 |
| Tru1I | TTAA | 2 cut(s) | 233, 429 |
| Tru9I | TTAA | 2 cut(s) | 233, 429 |
| TseFI | GTSAC | 1 cut(s) | 56 |
| Tsp45I | GTSAC | 1 cut(s) | 56 |
| TspDTI | ATGAA | 3 cut(s) | 17, 207, 357 |
| XceI | RCATGY | 1 cut(s) | 415 |
| XspI | CTAG | 3 cut(s) | 23, 197, 263 |