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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AciI | CCGC | 3 cut(s) | 174, 368, 372 |
| AcoI | YGGCCR | 1 cut(s) | 369 |
| AcsI | RAATTY | 1 cut(s) | 550 |
| AcuI | CTGAAG | 1 cut(s) | 201 |
| AfaI | GTAC | 1 cut(s) | 5 |
| AfiI | CCNNNNNNNGG | 3 cut(s) | 14, 260, 561 |
| AgsI | TTSAA | 2 cut(s) | 71, 349 |
| AjnI | CCWGG | 1 cut(s) | 259 |
| AluBI | AGCT | 4 cut(s) | 236, 365, 398, 434 |
| AluI | AGCT | 4 cut(s) | 236, 365, 398, 434 |
| AoxI | GGCC | 3 cut(s) | 369, 476, 505 |
| ApoI | RAATTY | 1 cut(s) | 550 |
| ArsI | GACNNNNNNTTYG | 4 cut(s) | 209, 241, 407, 439 |
| AspS9I | GGNCC | 1 cut(s) | 17 |
| AvaII | GGWCC | 1 cut(s) | 17 |
| BauI | CACGAG | 1 cut(s) | 472 |
| BbvCI | CCTCAGC | 1 cut(s) | 463 |
| BccI | CCATC | 3 cut(s) | 32, 312, 331 |
| BciT130I | CCWGG | 1 cut(s) | 261 |
| BclI | TGATCA | 1 cut(s) | 196 |
| BfaI | CTAG | 3 cut(s) | 53, 86, 357 |
| BfmI | CTRYAG | 1 cut(s) | 21 |
| Bme1390I | CCNGG | 1 cut(s) | 261 |
| Bme18I | GGWCC | 1 cut(s) | 17 |
| BmgT120I | GGNCC | 1 cut(s) | 17 |
| BmiI | GGNNCC | 1 cut(s) | 110 |
| BmrFI | CCNGG | 1 cut(s) | 261 |
| BmsI | GCATC | 3 cut(s) | 54, 362, 506 |
| Bpu10I | CCTNAGC | 1 cut(s) | 463 |
| BpuEI | CTTGAG | 1 cut(s) | 313 |
| BsaXI | ACNNNNNCTCC | 2 cut(s) | 463, 493 |
| Bsc4I | CCNNNNNNNGG | 3 cut(s) | 14, 260, 561 |
| BseBI | CCWGG | 1 cut(s) | 261 |
| BseGI | GGATG | 1 cut(s) | 163 |
| BseLI | CCNNNNNNNGG | 3 cut(s) | 14, 260, 561 |
| BseMII | CTCAG | 1 cut(s) | 477 |
| BseX3I | CGGCCG | 1 cut(s) | 369 |
| Bsh1285I | CGRYCG | 1 cut(s) | 372 |
| BshFI | GGCC | 3 cut(s) | 371, 478, 507 |
| BsiEI | CGRYCG | 1 cut(s) | 372 |
| BslI | CCNNNNNNNGG | 3 cut(s) | 14, 260, 561 |
| BsnI | GGCC | 3 cut(s) | 371, 478, 507 |
| Bsp143I | GATC | 2 cut(s) | 196, 527 |
| BspACI | CCGC | 3 cut(s) | 174, 368, 372 |
| BspANI | GGCC | 3 cut(s) | 371, 478, 507 |
| BspCNI | CTCAG | 1 cut(s) | 476 |
| BspLI | GGNNCC | 1 cut(s) | 110 |
| BssMI | GATC | 2 cut(s) | 196, 527 |
| BssSI | CACGAG | 1 cut(s) | 472 |
| Bst2BI | CACGAG | 1 cut(s) | 472 |
| Bst2UI | CCWGG | 1 cut(s) | 261 |
| Bst4CI | ACNGT | 1 cut(s) | 32 |
| Bst6I | CTCTTC | 1 cut(s) | 54 |
| BstDEI | CTNAG | 1 cut(s) | 463 |
| BstF5I | GGATG | 1 cut(s) | 163 |
| BstKTI | GATC | 2 cut(s) | 199, 530 |
| BstMBI | GATC | 2 cut(s) | 196, 527 |
| BstMCI | CGRYCG | 1 cut(s) | 372 |
| BstMWI | GCNNNNNNNGC | 9 cut(s) | 350, 371, 374, 380, 404, 407, 440, 443, 449 |
| BstNI | CCWGG | 1 cut(s) | 261 |
| BstSCI | CCNGG | 1 cut(s) | 259 |
| BstSFI | CTRYAG | 1 cut(s) | 21 |
| BstZI | CGGCCG | 1 cut(s) | 369 |
| BsuRI | GGCC | 3 cut(s) | 371, 478, 507 |
| BtsCI | GGATG | 1 cut(s) | 163 |
| BtsI | GCAGTG | 1 cut(s) | 148 |
| BtsIMutI | CAGTG | 2 cut(s) | 37, 148 |
| CciNI | GCGGCCGC | 1 cut(s) | 369 |
| Cfr13I | GGNCC | 1 cut(s) | 17 |
| Csp6I | GTAC | 1 cut(s) | 4 |
| CviQI | GTAC | 1 cut(s) | 4 |
| DdeI | CTNAG | 1 cut(s) | 463 |
| DpnI | GATC | 2 cut(s) | 198, 529 |
| DpnII | GATC | 2 cut(s) | 196, 527 |
| EaeI | YGGCCR | 1 cut(s) | 369 |
| EagI | CGGCCG | 1 cut(s) | 369 |
| Eam1104I | CTCTTC | 1 cut(s) | 54 |
| EarI | CTCTTC | 1 cut(s) | 54 |
| EclXI | CGGCCG | 1 cut(s) | 369 |
| Eco147I | AGGCCT | 1 cut(s) | 478 |
| Eco47I | GGWCC | 1 cut(s) | 17 |
| Eco52I | CGGCCG | 1 cut(s) | 369 |
| Eco57I | CTGAAG | 1 cut(s) | 201 |
| EcoO109I | RGGNCCY | 1 cut(s) | 17 |
| EcoRI | GAATTC | 1 cut(s) | 550 |
| EcoRII | CCWGG | 1 cut(s) | 259 |
| FaiI | YATR | 7 cut(s) | 77, 93, 95, 170, 195, 204, 242 |
| FalI | AAGNNNNNCTT | 4 cut(s) | 51, 83, 275, 307 |
| FauI | CCCGC | 1 cut(s) | 181 |
| FbaI | TGATCA | 1 cut(s) | 196 |
| FokI | GGATG | 1 cut(s) | 170 |
| FspBI | CTAG | 3 cut(s) | 53, 86, 357 |
| HaeIII | GGCC | 3 cut(s) | 371, 478, 507 |
| Hpy166II | GTNNAC | 1 cut(s) | 426 |
| Hpy188I | TCNGA | 1 cut(s) | 483 |
| Hpy188III | TCNNGA | 5 cut(s) | 53, 71, 86, 357, 525 |
| Hpy8I | GTNNAC | 1 cut(s) | 426 |
| Hpy99I | CGWCG | 1 cut(s) | 221 |
| HpyAV | CCTTC | 3 cut(s) | 8, 343, 531 |
| HpyCH4III | ACNGT | 1 cut(s) | 32 |
| HpyCH4V | TGCA | 2 cut(s) | 97, 344 |
| HpyF10VI | GCNNNNNNNGC | 9 cut(s) | 350, 371, 374, 380, 404, 407, 440, 443, 449 |
| HpyF3I | CTNAG | 1 cut(s) | 463 |
| Ksp22I | TGATCA | 1 cut(s) | 196 |
| Kzo9I | GATC | 2 cut(s) | 196, 527 |
| LpnPI | CCDG | 6 cut(s) | 33, 129, 246, 273, 393, 538 |
| LweI | GCATC | 3 cut(s) | 54, 362, 506 |
| MaeI | CTAG | 3 cut(s) | 53, 86, 357 |
| MalI | GATC | 2 cut(s) | 198, 529 |
| MboI | GATC | 2 cut(s) | 196, 527 |
| MboII | GAAGA | 7 cut(s) | 23, 71, 137, 194, 276, 343, 346 |
| MluCI | AATT | 1 cut(s) | 550 |
| MmeI | TCCRAC | 2 cut(s) | 506, 539 |
| MnlI | CCTC | 6 cut(s) | 148, 223, 288, 468, 472, 489 |
| MspA1I | CMGCKG | 2 cut(s) | 176, 374 |
| MspR9I | CCNGG | 1 cut(s) | 261 |
| MvaI | CCWGG | 1 cut(s) | 261 |
| MwoI | GCNNNNNNNGC | 9 cut(s) | 350, 371, 374, 380, 404, 407, 440, 443, 449 |
| NdeII | GATC | 2 cut(s) | 196, 527 |
| NlaIV | GGNNCC | 1 cut(s) | 110 |
| NotI | GCGGCCGC | 1 cut(s) | 369 |
| PceI | AGGCCT | 1 cut(s) | 478 |
| PcsI | WCGNNNNNNNCGW | 2 cut(s) | 225, 479 |
| PpuMI | RGGWCCY | 1 cut(s) | 17 |
| Psp5II | RGGWCCY | 1 cut(s) | 17 |
| Psp6I | CCWGG | 1 cut(s) | 259 |
| PspGI | CCWGG | 1 cut(s) | 259 |
| PspN4I | GGNNCC | 1 cut(s) | 110 |
| PspPI | GGNCC | 1 cut(s) | 17 |
| PspPPI | RGGWCCY | 1 cut(s) | 17 |
| RsaI | GTAC | 1 cut(s) | 5 |
| RsaNI | GTAC | 1 cut(s) | 4 |
| Sau3AI | GATC | 2 cut(s) | 196, 527 |
| Sau96I | GGNCC | 1 cut(s) | 17 |
| ScrFI | CCNGG | 1 cut(s) | 261 |
| SetI | ASST | 8 cut(s) | 19, 238, 262, 367, 400, 436, 464, 523 |
| SfaNI | GCATC | 3 cut(s) | 54, 362, 506 |
| SfcI | CTRYAG | 1 cut(s) | 21 |
| SinI | GGWCC | 1 cut(s) | 17 |
| SmlI | CTYRAG | 1 cut(s) | 292 |
| SmoI | CTYRAG | 1 cut(s) | 292 |
| Sse9I | AATT | 1 cut(s) | 550 |
| SseBI | AGGCCT | 1 cut(s) | 478 |
| SsiI | CCGC | 3 cut(s) | 174, 368, 372 |
| SspMI | CTAG | 3 cut(s) | 53, 86, 357 |
| StuI | AGGCCT | 1 cut(s) | 478 |
| StyD4I | CCNGG | 1 cut(s) | 259 |
| TaaI | ACNGT | 1 cut(s) | 32 |
| TaqI | TCGA | 1 cut(s) | 228 |
| TasI | AATT | 1 cut(s) | 550 |
| TauI | GCSGC | 2 cut(s) | 371, 374 |
| TscAI | CASTG | 2 cut(s) | 37, 148 |
| TspDTI | ATGAA | 4 cut(s) | 72, 144, 177, 204 |
| TspRI | CASTG | 2 cut(s) | 37, 148 |
| VpaK11BI | GGWCC | 1 cut(s) | 17 |
| XapI | RAATTY | 1 cut(s) | 550 |
| XbaI | TCTAGA | 3 cut(s) | 52, 85, 356 |
| XspI | CTAG | 3 cut(s) | 53, 86, 357 |