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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AdeI | CACNNNGTG | 1 cut(s) | 503 |
| AfaI | GTAC | 1 cut(s) | 201 |
| AfiI | CCNNNNNNNGG | 1 cut(s) | 241 |
| AgsI | TTSAA | 3 cut(s) | 98, 376, 509 |
| AjnI | CCWGG | 1 cut(s) | 347 |
| AluBI | AGCT | 5 cut(s) | 317, 371, 419, 452, 488 |
| AluI | AGCT | 5 cut(s) | 317, 371, 419, 452, 488 |
| AoxI | GGCC | 1 cut(s) | 350 |
| ApeKI | GCWGC | 2 cut(s) | 464, 494 |
| AsuHPI | GGTGA | 2 cut(s) | 251, 337 |
| AsuNHI | GCTAGC | 1 cut(s) | 5 |
| BbvI | GCAGC | 2 cut(s) | 451, 481 |
| BciT130I | CCWGG | 1 cut(s) | 349 |
| BfaI | CTAG | 5 cut(s) | 6, 57, 314, 318, 408 |
| BisI | GCNGC | 2 cut(s) | 465, 495 |
| BlsI | GCNGC | 2 cut(s) | 466, 496 |
| Bme1390I | CCNGG | 1 cut(s) | 349 |
| BmrFI | CCNGG | 1 cut(s) | 349 |
| BmsI | GCATC | 1 cut(s) | 261 |
| BmtI | GCTAGC | 1 cut(s) | 9 |
| BsaJI | CCNNGG | 2 cut(s) | 235, 347 |
| BsaXI | ACNNNNNCTCC | 2 cut(s) | 135, 165 |
| Bsc4I | CCNNNNNNNGG | 1 cut(s) | 241 |
| Bse1I | ACTGG | 3 cut(s) | 10, 165, 187 |
| BseBI | CCWGG | 1 cut(s) | 349 |
| BseDI | CCNNGG | 2 cut(s) | 235, 347 |
| BseLI | CCNNNNNNNGG | 1 cut(s) | 241 |
| BseMII | CTCAG | 2 cut(s) | 411, 444 |
| BseNI | ACTGG | 3 cut(s) | 10, 165, 187 |
| BseRI | GAGGAG | 1 cut(s) | 452 |
| BseXI | GCAGC | 2 cut(s) | 451, 481 |
| BsgI | GTGCAG | 1 cut(s) | 480 |
| BshFI | GGCC | 1 cut(s) | 352 |
| BslI | CCNNNNNNNGG | 1 cut(s) | 241 |
| BsnI | GGCC | 1 cut(s) | 352 |
| Bsp143I | GATC | 1 cut(s) | 91 |
| BspANI | GGCC | 1 cut(s) | 352 |
| BspCNI | CTCAG | 2 cut(s) | 412, 445 |
| BspOI | GCTAGC | 1 cut(s) | 9 |
| BsrI | ACTGG | 3 cut(s) | 10, 165, 187 |
| BssECI | CCNNGG | 2 cut(s) | 235, 347 |
| BssMI | GATC | 1 cut(s) | 91 |
| BssT1I | CCWWGG | 1 cut(s) | 235 |
| Bst2UI | CCWGG | 1 cut(s) | 349 |
| Bst6I | CTCTTC | 2 cut(s) | 395, 473 |
| BstC8I | GCNNGC | 2 cut(s) | 7, 232 |
| BstDEI | CTNAG | 3 cut(s) | 420, 453, 500 |
| BstKTI | GATC | 1 cut(s) | 94 |
| BstMBI | GATC | 1 cut(s) | 91 |
| BstMWI | GCNNNNNNNGC | 2 cut(s) | 304, 494 |
| BstNI | CCWGG | 1 cut(s) | 349 |
| BstNSI | RCATGY | 1 cut(s) | 228 |
| BstSCI | CCNGG | 1 cut(s) | 347 |
| BstV1I | GCAGC | 2 cut(s) | 451, 481 |
| BsuRI | GGCC | 1 cut(s) | 352 |
| Cac8I | GCNNGC | 2 cut(s) | 7, 232 |
| Csp6I | GTAC | 1 cut(s) | 200 |
| CviAII | CATG | 2 cut(s) | 211, 225 |
| CviQI | GTAC | 1 cut(s) | 200 |
| DdeI | CTNAG | 3 cut(s) | 420, 453, 500 |
| DpnI | GATC | 1 cut(s) | 93 |
| DpnII | GATC | 1 cut(s) | 91 |
| DraIII | CACNNNGTG | 1 cut(s) | 503 |
| Eam1104I | CTCTTC | 2 cut(s) | 395, 473 |
| EarI | CTCTTC | 2 cut(s) | 395, 473 |
| Eco130I | CCWWGG | 1 cut(s) | 235 |
| EcoRII | CCWGG | 1 cut(s) | 347 |
| EcoT14I | CCWWGG | 1 cut(s) | 235 |
| ErhI | CCWWGG | 1 cut(s) | 235 |
| FaeI | CATG | 2 cut(s) | 214, 228 |
| FaiI | YATR | 9 cut(s) | 16, 18, 28, 30, 212, 226, 282, 284, 395 |
| FalI | AAGNNNNNCTT | 2 cut(s) | 355, 387 |
| FatI | CATG | 2 cut(s) | 210, 224 |
| FauNDI | CATATG | 1 cut(s) | 282 |
| Fnu4HI | GCNGC | 2 cut(s) | 465, 495 |
| Fsp4HI | GCNGC | 2 cut(s) | 465, 495 |
| FspBI | CTAG | 5 cut(s) | 6, 57, 314, 318, 408 |
| GluI | GCNGC | 2 cut(s) | 465, 495 |
| HaeIII | GGCC | 1 cut(s) | 352 |
| Hin1II | CATG | 2 cut(s) | 214, 228 |
| HindIII | AAGCTT | 2 cut(s) | 369, 486 |
| HinfI | GANTC | 1 cut(s) | 481 |
| HphI | GGTGA | 2 cut(s) | 251, 337 |
| Hpy166II | GTNNAC | 3 cut(s) | 23, 174, 218 |
| Hpy188III | TCNNGA | 2 cut(s) | 57, 95 |
| Hpy8I | GTNNAC | 3 cut(s) | 23, 174, 218 |
| HpyAV | CCTTC | 1 cut(s) | 315 |
| HpyCH4V | TGCA | 5 cut(s) | 41, 68, 230, 274, 497 |
| HpyF10VI | GCNNNNNNNGC | 2 cut(s) | 304, 494 |
| HpyF3I | CTNAG | 3 cut(s) | 420, 453, 500 |
| Hsp92II | CATG | 2 cut(s) | 214, 228 |
| Kzo9I | GATC | 1 cut(s) | 91 |
| LpnPI | CCDG | 9 cut(s) | 23, 99, 168, 178, 216, 236, 334, 361, 371 |
| Lsp1109I | GCAGC | 2 cut(s) | 451, 481 |
| LweI | GCATC | 1 cut(s) | 261 |
| MaeI | CTAG | 5 cut(s) | 6, 57, 314, 318, 408 |
| MaeIII | GTNAC | 1 cut(s) | 287 |
| MalI | GATC | 1 cut(s) | 93 |
| MboI | GATC | 1 cut(s) | 91 |
| MboII | GAAGA | 5 cut(s) | 110, 412, 490, 521, 545 |
| MluCI | AATT | 1 cut(s) | 470 |
| MlyI | GAGTC | 1 cut(s) | 490 |
| MseI | TTAA | 2 cut(s) | 129, 339 |
| MslI | CAYNNNNRTG | 1 cut(s) | 223 |
| MspR9I | CCNGG | 1 cut(s) | 349 |
| MvaI | CCWGG | 1 cut(s) | 349 |
| MwoI | GCNNNNNNNGC | 2 cut(s) | 304, 494 |
| NdeI | CATATG | 1 cut(s) | 282 |
| NdeII | GATC | 1 cut(s) | 91 |
| NheI | GCTAGC | 1 cut(s) | 5 |
| NlaIII | CATG | 2 cut(s) | 214, 228 |
| NspI | RCATGY | 1 cut(s) | 228 |
| PkrI | GCNGC | 2 cut(s) | 466, 496 |
| PleI | GAGTC | 1 cut(s) | 489 |
| PpsI | GAGTC | 1 cut(s) | 489 |
| Psp6I | CCWGG | 1 cut(s) | 347 |
| PspGI | CCWGG | 1 cut(s) | 347 |
| RsaI | GTAC | 1 cut(s) | 201 |
| RsaNI | GTAC | 1 cut(s) | 200 |
| RseI | CAYNNNNRTG | 1 cut(s) | 223 |
| SaqAI | TTAA | 2 cut(s) | 129, 339 |
| SatI | GCNGC | 2 cut(s) | 465, 495 |
| Sau3AI | GATC | 1 cut(s) | 91 |
| SchI | GAGTC | 1 cut(s) | 490 |
| ScrFI | CCNGG | 1 cut(s) | 349 |
| SetI | ASST | 9 cut(s) | 118, 241, 246, 315, 319, 373, 421, 454, 490 |
| SfaNI | GCATC | 1 cut(s) | 261 |
| SmiMI | CAYNNNNRTG | 1 cut(s) | 223 |
| Sse9I | AATT | 1 cut(s) | 470 |
| SspI | AATATT | 1 cut(s) | 196 |
| SspMI | CTAG | 5 cut(s) | 6, 57, 314, 318, 408 |
| StyD4I | CCNGG | 1 cut(s) | 347 |
| StyI | CCWWGG | 1 cut(s) | 235 |
| TaqI | TCGA | 1 cut(s) | 435 |
| TasI | AATT | 1 cut(s) | 470 |
| Tru1I | TTAA | 2 cut(s) | 129, 339 |
| Tru9I | TTAA | 2 cut(s) | 129, 339 |
| TseI | GCWGC | 2 cut(s) | 464, 494 |
| XbaI | TCTAGA | 1 cut(s) | 56 |
| XceI | RCATGY | 1 cut(s) | 228 |
| XspI | CTAG | 5 cut(s) | 6, 57, 314, 318, 408 |