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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AciI | CCGC | 3 cut(s) | 66, 578, 589 |
| AclWI | GGATC | 2 cut(s) | 44, 292 |
| AcsI | RAATTY | 3 cut(s) | 268, 466, 515 |
| AcuI | CTGAAG | 1 cut(s) | 305 |
| AgsI | TTSAA | 3 cut(s) | 75, 373, 511 |
| AluBI | AGCT | 3 cut(s) | 319, 560, 573 |
| AluI | AGCT | 3 cut(s) | 319, 560, 573 |
| AlwI | GGATC | 2 cut(s) | 44, 292 |
| AoxI | GGCC | 1 cut(s) | 246 |
| ApeKI | GCWGC | 1 cut(s) | 557 |
| ApoI | RAATTY | 3 cut(s) | 268, 466, 515 |
| AseI | ATTAAT | 1 cut(s) | 188 |
| Asp700I | GAANNNNTTC | 1 cut(s) | 238 |
| AspS9I | GGNCC | 2 cut(s) | 21, 246 |
| AsuHPI | GGTGA | 4 cut(s) | 25, 439, 499, 578 |
| AvaII | GGWCC | 1 cut(s) | 21 |
| BanII | GRGCYC | 1 cut(s) | 536 |
| BbsI | GAAGAC | 1 cut(s) | 23 |
| BbvI | GCAGC | 1 cut(s) | 569 |
| BccI | CCATC | 1 cut(s) | 629 |
| BceAI | ACGGC | 1 cut(s) | 86 |
| BcgI | CGANNNNNNTGC | 2 cut(s) | 96, 130 |
| BisI | GCNGC | 1 cut(s) | 558 |
| BlpI | GCTNAGC | 1 cut(s) | 561 |
| BlsI | GCNGC | 1 cut(s) | 559 |
| Bme18I | GGWCC | 1 cut(s) | 21 |
| BmgT120I | GGNCC | 2 cut(s) | 21, 246 |
| BmiI | GGNNCC | 1 cut(s) | 23 |
| BmsI | GCATC | 2 cut(s) | 111, 488 |
| BpiI | GAAGAC | 1 cut(s) | 23 |
| Bpu1102I | GCTNAGC | 1 cut(s) | 561 |
| Bsa29I | ATCGAT | 1 cut(s) | 48 |
| BsaJI | CCNNGG | 2 cut(s) | 35, 354 |
| BseCI | ATCGAT | 1 cut(s) | 48 |
| BseDI | CCNNGG | 2 cut(s) | 35, 354 |
| BseMII | CTCAG | 1 cut(s) | 575 |
| BseRI | GAGGAG | 2 cut(s) | 347, 350 |
| BseXI | GCAGC | 1 cut(s) | 569 |
| BshFI | GGCC | 1 cut(s) | 248 |
| BshVI | ATCGAT | 1 cut(s) | 48 |
| BsiSI | CCGG | 1 cut(s) | 63 |
| BslFI | GGGAC | 1 cut(s) | 7 |
| BsmFI | GGGAC | 1 cut(s) | 7 |
| BsmI | GAATGC | 1 cut(s) | 114 |
| BsnI | GGCC | 1 cut(s) | 248 |
| Bsp1286I | GDGCHC | 1 cut(s) | 536 |
| Bsp143I | GATC | 4 cut(s) | 49, 125, 279, 284 |
| Bsp1720I | GCTNAGC | 1 cut(s) | 561 |
| BspACI | CCGC | 3 cut(s) | 66, 578, 589 |
| BspANI | GGCC | 1 cut(s) | 248 |
| BspCNI | CTCAG | 1 cut(s) | 574 |
| BspDI | ATCGAT | 1 cut(s) | 48 |
| BspLI | GGNNCC | 1 cut(s) | 23 |
| BspPI | GGATC | 2 cut(s) | 44, 292 |
| BssECI | CCNNGG | 2 cut(s) | 35, 354 |
| BssMI | GATC | 4 cut(s) | 49, 125, 279, 284 |
| Bst4CI | ACNGT | 1 cut(s) | 355 |
| BstC8I | GCNNGC | 1 cut(s) | 262 |
| BstDEI | CTNAG | 2 cut(s) | 404, 561 |
| BstDSI | CCRYGG | 1 cut(s) | 354 |
| BstKTI | GATC | 4 cut(s) | 52, 128, 282, 287 |
| BstMBI | GATC | 4 cut(s) | 49, 125, 279, 284 |
| BstV1I | GCAGC | 1 cut(s) | 569 |
| BstV2I | GAAGAC | 1 cut(s) | 23 |
| BstX2I | RGATCY | 1 cut(s) | 284 |
| BstYI | RGATCY | 1 cut(s) | 284 |
| Bsu15I | ATCGAT | 1 cut(s) | 48 |
| BsuRI | GGCC | 1 cut(s) | 248 |
| BsuTUI | ATCGAT | 1 cut(s) | 48 |
| BtgI | CCRYGG | 1 cut(s) | 354 |
| Cac8I | GCNNGC | 1 cut(s) | 262 |
| Cfr13I | GGNCC | 2 cut(s) | 21, 246 |
| ClaI | ATCGAT | 1 cut(s) | 48 |
| CviAII | CATG | 2 cut(s) | 243, 424 |
| CviJI | RGCY | 7 cut(s) | 101, 248, 260, 319, 534, 560, 573 |
| CviKI_1 | RGCY | 7 cut(s) | 101, 248, 260, 319, 534, 560, 573 |
| DdeI | CTNAG | 2 cut(s) | 404, 561 |
| DpnI | GATC | 4 cut(s) | 51, 127, 281, 286 |
| DpnII | GATC | 4 cut(s) | 49, 125, 279, 284 |
| Eco24I | GRGCYC | 1 cut(s) | 536 |
| Eco47I | GGWCC | 1 cut(s) | 21 |
| Eco57I | CTGAAG | 1 cut(s) | 305 |
| EcoT38I | GRGCYC | 1 cut(s) | 536 |
| FaeI | CATG | 2 cut(s) | 246, 427 |
| FaiI | YATR | 8 cut(s) | 45, 209, 244, 291, 348, 350, 425, 628 |
| FaqI | GGGAC | 1 cut(s) | 7 |
| FatI | CATG | 2 cut(s) | 242, 423 |
| FauI | CCCGC | 1 cut(s) | 585 |
| Fnu4HI | GCNGC | 1 cut(s) | 558 |
| FriOI | GRGCYC | 1 cut(s) | 536 |
| Fsp4HI | GCNGC | 1 cut(s) | 558 |
| GluI | GCNGC | 1 cut(s) | 558 |
| HaeIII | GGCC | 1 cut(s) | 248 |
| HapII | CCGG | 1 cut(s) | 63 |
| Hin1II | CATG | 2 cut(s) | 246, 427 |
| HinfI | GANTC | 1 cut(s) | 541 |
| HpaII | CCGG | 1 cut(s) | 63 |
| HphI | GGTGA | 4 cut(s) | 25, 439, 499, 578 |
| Hpy188I | TCNGA | 4 cut(s) | 36, 54, 284, 324 |
| HpyAV | CCTTC | 3 cut(s) | 146, 160, 505 |
| HpyCH4III | ACNGT | 1 cut(s) | 355 |
| HpyCH4IV | ACGT | 1 cut(s) | 252 |
| HpyCH4V | TGCA | 4 cut(s) | 43, 117, 207, 479 |
| HpyF3I | CTNAG | 2 cut(s) | 404, 561 |
| HpySE526I | ACGT | 1 cut(s) | 252 |
| Hsp92II | CATG | 2 cut(s) | 246, 427 |
| Kzo9I | GATC | 4 cut(s) | 49, 125, 279, 284 |
| LmnI | GCTCC | 1 cut(s) | 578 |
| LpnPI | CCDG | 4 cut(s) | 76, 182, 274, 280 |
| Lsp1109I | GCAGC | 1 cut(s) | 569 |
| LweI | GCATC | 2 cut(s) | 111, 488 |
| MaeII | ACGT | 1 cut(s) | 252 |
| MaeIII | GTNAC | 1 cut(s) | 457 |
| MalI | GATC | 4 cut(s) | 51, 127, 281, 286 |
| MboI | GATC | 4 cut(s) | 49, 125, 279, 284 |
| MboII | GAAGA | 4 cut(s) | 23, 175, 385, 612 |
| MflI | RGATCY | 1 cut(s) | 284 |
| MhlI | GDGCHC | 1 cut(s) | 536 |
| MluCI | AATT | 8 cut(s) | 87, 237, 268, 367, 411, 466, 506, 515 |
| MlyI | GAGTC | 1 cut(s) | 535 |
| MmeI | TCCRAC | 2 cut(s) | 77, 163 |
| MroXI | GAANNNNTTC | 1 cut(s) | 238 |
| MseI | TTAA | 3 cut(s) | 90, 188, 414 |
| MspI | CCGG | 1 cut(s) | 63 |
| Mva1269I | GAATGC | 1 cut(s) | 114 |
| NdeII | GATC | 4 cut(s) | 49, 125, 279, 284 |
| NlaIII | CATG | 2 cut(s) | 246, 427 |
| NlaIV | GGNNCC | 1 cut(s) | 23 |
| NmuCI | GTSAC | 1 cut(s) | 457 |
| PctI | GAATGC | 1 cut(s) | 114 |
| PdmI | GAANNNNTTC | 1 cut(s) | 238 |
| PkrI | GCNGC | 1 cut(s) | 559 |
| PleI | GAGTC | 1 cut(s) | 535 |
| PpsI | GAGTC | 1 cut(s) | 535 |
| PshBI | ATTAAT | 1 cut(s) | 188 |
| PspN4I | GGNNCC | 1 cut(s) | 23 |
| PspPI | GGNCC | 2 cut(s) | 21, 246 |
| PsuI | RGATCY | 1 cut(s) | 284 |
| SaqAI | TTAA | 3 cut(s) | 90, 188, 414 |
| SatI | GCNGC | 1 cut(s) | 558 |
| Sau3AI | GATC | 4 cut(s) | 49, 125, 279, 284 |
| Sau96I | GGNCC | 2 cut(s) | 21, 246 |
| SchI | GAGTC | 1 cut(s) | 535 |
| SduI | GDGCHC | 1 cut(s) | 536 |
| SetI | ASST | 8 cut(s) | 15, 255, 321, 504, 551, 562, 575, 586 |
| SfaNI | GCATC | 2 cut(s) | 111, 488 |
| SinI | GGWCC | 1 cut(s) | 21 |
| Sse9I | AATT | 8 cut(s) | 87, 237, 268, 367, 411, 466, 506, 515 |
| SsiI | CCGC | 3 cut(s) | 66, 578, 589 |
| SspI | AATATT | 1 cut(s) | 528 |
| TaaI | ACNGT | 1 cut(s) | 355 |
| TaiI | ACGT | 1 cut(s) | 255 |
| TaqI | TCGA | 1 cut(s) | 48 |
| TaqII | GACCGA | 1 cut(s) | 476 |
| TasI | AATT | 8 cut(s) | 87, 237, 268, 367, 411, 466, 506, 515 |
| Tru1I | TTAA | 3 cut(s) | 90, 188, 414 |
| Tru9I | TTAA | 3 cut(s) | 90, 188, 414 |
| TseFI | GTSAC | 1 cut(s) | 457 |
| TseI | GCWGC | 1 cut(s) | 557 |
| Tsp45I | GTSAC | 1 cut(s) | 457 |
| TspDTI | ATGAA | 1 cut(s) | 231 |
| TspGWI | ACGGA | 1 cut(s) | 449 |
| VpaK11BI | GGWCC | 1 cut(s) | 21 |
| VspI | ATTAAT | 1 cut(s) | 188 |
| XapI | RAATTY | 3 cut(s) | 268, 466, 515 |
| XmnI | GAANNNNTTC | 1 cut(s) | 238 |