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Sequences greater than 6 bases
| Enzymes | Recognition Sequence | |
| Aar I | CACCTGC (4/8) | |
| Alo I | (7/12) GAACNNNNNNTCC (12/7) | |
| D | Asc I | GG/CGCGCC |
| D | AsiS I | GCGAT/CGC |
| D | Bae I | (10/15) ACNNNNGTAYC (12/7) |
| D | BbvC I | CCTCAGC (-5/-2) |
| D | CspC I | CAANNNNNGTGG |
| D | Fse I | GGCCGG/CC |
| FspA I | RTGC/GCAY | |
| D | Not I | GC/GGCCGC |
| D | Pac I | TTAAT/TAA |
| X | Pas I | CC/CWGGG |
| D | Pme I | GTTT/AAAC |
| Ppi I | (7/12) GAACNNNNNCTC (13/8) | |
| D | PpuM I | RG/GWCCY |
| D | PspX I | VC/TCGAGB |
| Psr I | (7/12) GAACNNNNNNTAC (12/7) | |
| D | Rsr II | CG/GWCCG |
| SanD I | GG/GWCCC | |
| D | Sap I | GCTCTTC (1/4) |
| D | Sbf I | CCTGCA/GG |
| D | SexA I | A/CCWGGT |
| D | Sfi I | GGCCNNNN/NGGCC |
| D | SgrA I | CR/CCGGYG |
| Srf I | GCCC/GGGC | |
| X | Sse232 I | CG/CCGGCG |
| X | Sse8647 I | AG/GWCCT |
| D | Swa I | ATTT/AAAT |
| X | UbaF2 I | GAAAYNNNNNRTG |
In addition, see homing endonucleases.
Note:
Enzymes marked with an ( D ) are
available from NEB.
Enzymes marked with an ( X ) are not currently commercially available.