Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks
| Domain Name | Pfam ID | Position | E-value | Description |
|---|---|---|---|---|
| DNA_gyraseB | PF00204 | 269 - 362 | 1.7e-21 | DNA gyrase B |
| Toprim | PF01751 | 426 - 524 | 4.8e-07 | Toprim domain |
| TOPRIM_C | PF16898 | 540 - 667 | 7.9e-47 | C-terminal associated domain of TOPRIM |
| DNA_topoisoIV | PF00521 | 670 - 1129 | 7.1e-116 | DNA gyrase/topoisomerase IV, subunit A |
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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AanI | TTATAA | 2 cut(s) | 2472, 2685 |
| AarI | CACCTGC | 1 cut(s) | 502 |
| AasI | GACNNNNNNGTC | 1 cut(s) | 146 |
| Acc36I | ACCTGC | 4 cut(s) | 51, 502, 3325, 3695 |
| AccB1I | GGYRCC | 3 cut(s) | 302, 366, 434 |
| AcsI | RAATTY | 9 cut(s) | 464, 614, 2646, 2690, 2781, 2843, 2931, 2942, 2963 |
| AcuI | CTGAAG | 3 cut(s) | 3201, 3905, 3909 |
| AcvI | CACGTG | 1 cut(s) | 1006 |
| AcyI | GRCGYC | 2 cut(s) | 303, 435 |
| AfiI | CCNNNNNNNGG | 6 cut(s) | 1072, 1367, 2152, 3007, 3593, 3704 |
| AgeI | ACCGGT | 1 cut(s) | 413 |
| AjnI | CCWGG | 4 cut(s) | 54, 1915, 2041, 2387 |
| AjuI | GAANNNNNNNTTGG | 4 cut(s) | 2720, 2752, 2975, 3007 |
| AleI | CACNNNNGTG | 1 cut(s) | 2148 |
| AloI | GAACNNNNNNTCC | 2 cut(s) | 344, 376 |
| Alw21I | GWGCWC | 4 cut(s) | 1005, 2281, 2456, 3111 |
| Alw26I | GTCTC | 3 cut(s) | 166, 2475, 2627 |
| AlwNI | CAGNNNCTG | 1 cut(s) | 121 |
| Ama87I | CYCGRG | 4 cut(s) | 173, 585, 1682, 1708 |
| AoxI | GGCC | 5 cut(s) | 77, 1580, 2724, 3845, 3928 |
| ApoI | RAATTY | 9 cut(s) | 464, 614, 2646, 2690, 2781, 2843, 2931, 2942, 2963 |
| AseI | ATTAAT | 1 cut(s) | 2214 |
| AsiGI | ACCGGT | 1 cut(s) | 413 |
| Asp700I | GAANNNNTTC | 5 cut(s) | 278, 1170, 2931, 2946, 3122 |
| AspLEI | GCGC | 3 cut(s) | 66, 305, 437 |
| AspS9I | GGNCC | 9 cut(s) | 78, 148, 582, 727, 1342, 1581, 1731, 2673, 3788 |
| AsuC2I | CCSGG | 7 cut(s) | 174, 175, 307, 586, 587, 3417, 3912 |
| AvaI | CYCGRG | 4 cut(s) | 173, 585, 1682, 1708 |
| AvaII | GGWCC | 7 cut(s) | 148, 582, 727, 1342, 1731, 2673, 3788 |
| AxyI | CCTNAGG | 1 cut(s) | 2799 |
| BaeGI | GKGCMC | 1 cut(s) | 369 |
| BamHI | GGATCC | 3 cut(s) | 232, 2536, 2731 |
| BanI | GGYRCC | 3 cut(s) | 302, 366, 434 |
| BanII | GRGCYC | 3 cut(s) | 180, 2456, 3111 |
| BbrPI | CACGTG | 1 cut(s) | 1006 |
| BbsI | GAAGAC | 5 cut(s) | 121, 413, 1163, 1202, 3592 |
| Bbv12I | GWGCWC | 4 cut(s) | 1005, 2281, 2456, 3111 |
| BceAI | ACGGC | 3 cut(s) | 316, 442, 502 |
| BcgI | CGANNNNNNTGC | 2 cut(s) | 172, 206 |
| BciT130I | CCWGG | 4 cut(s) | 56, 1917, 2043, 2389 |
| BclI | TGATCA | 3 cut(s) | 1509, 1519, 1930 |
| BcnI | CCSGG | 7 cut(s) | 174, 175, 307, 586, 587, 3417, 3912 |
| BcoDI | GTCTC | 3 cut(s) | 166, 2475, 2627 |
| BfaI | CTAG | 5 cut(s) | 786, 1244, 1799, 2786, 3798 |
| BfmI | CTRYAG | 3 cut(s) | 44, 1454, 2775 |
| BfoI | RGCGCY | 2 cut(s) | 306, 438 |
| BfuAI | ACCTGC | 4 cut(s) | 51, 502, 3325, 3695 |
| BlpI | GCTNAGC | 1 cut(s) | 2127 |
| BmcAI | AGTACT | 4 cut(s) | 1742, 1765, 2170, 2773 |
| Bme18I | GGWCC | 7 cut(s) | 148, 582, 727, 1342, 1731, 2673, 3788 |
| BmeT110I | CYCGRG | 4 cut(s) | 173, 585, 1682, 1708 |
| BmgT120I | GGNCC | 9 cut(s) | 78, 148, 582, 727, 1342, 1581, 1731, 2673, 3788 |
| BmrI | ACTGGG | 1 cut(s) | 2101 |
| BmsI | GCATC | 5 cut(s) | 674, 1225, 1510, 3379, 3885 |
| BmuI | ACTGGG | 1 cut(s) | 2101 |
| BpiI | GAAGAC | 5 cut(s) | 121, 413, 1163, 1202, 3592 |
| BpmI | CTGGAG | 4 cut(s) | 1250, 2470, 2717, 2907 |
| Bpu10I | CCTNAGC | 2 cut(s) | 999, 1302 |
| Bpu1102I | GCTNAGC | 1 cut(s) | 2127 |
| BpuEI | CTTGAG | 8 cut(s) | 236, 394, 2957, 3023, 3125, 3290, 3428, 3795 |
| BpuMI | CCSGG | 7 cut(s) | 174, 175, 307, 586, 587, 3417, 3912 |
| Bsa29I | ATCGAT | 1 cut(s) | 98 |
| BsaAI | YACGTR | 1 cut(s) | 1006 |
| BsaBI | GATNNNNATC | 2 cut(s) | 1239, 1524 |
| BsaHI | GRCGYC | 2 cut(s) | 303, 435 |
| BsaWI | WCCGGW | 1 cut(s) | 413 |
| BsaXI | ACNNNNNCTCC | 4 cut(s) | 344, 374, 1520, 1550 |
| Bsc4I | CCNNNNNNNGG | 6 cut(s) | 1072, 1367, 2152, 3007, 3593, 3704 |
| Bse118I | RCCGGY | 2 cut(s) | 75, 413 |
| Bse1I | ACTGG | 9 cut(s) | 285, 548, 584, 2107, 2166, 2399, 2415, 2563, 3543 |
| Bse21I | CCTNAGG | 1 cut(s) | 2799 |
| Bse3DI | GCAATG | 5 cut(s) | 891, 1320, 1570, 3558, 3623 |
| Bse8I | GATNNNNATC | 2 cut(s) | 1239, 1524 |
| BseBI | CCWGG | 4 cut(s) | 56, 1917, 2043, 2389 |
| BseCI | ATCGAT | 1 cut(s) | 98 |
| BseGI | GGATG | 6 cut(s) | 689, 813, 1240, 2338, 2460, 3571 |
| BseJI | GATNNNNATC | 2 cut(s) | 1239, 1524 |
| BseLI | CCNNNNNNNGG | 6 cut(s) | 1072, 1367, 2152, 3007, 3593, 3704 |
| BseMI | GCAATG | 5 cut(s) | 891, 1320, 1570, 3558, 3623 |
| BseMII | CTCAG | 7 cut(s) | 990, 1658, 2118, 2656, 2790, 3222, 3279 |
| BseNI | ACTGG | 9 cut(s) | 285, 548, 584, 2107, 2166, 2399, 2415, 2563, 3543 |
| BseRI | GAGGAG | 4 cut(s) | 2816, 3425, 3955, 3958 |
| BseSI | GKGCMC | 1 cut(s) | 369 |
| BseYI | CCCAGC | 1 cut(s) | 1319 |
| Bsh1285I | CGRYCG | 1 cut(s) | 30 |
| BshFI | GGCC | 5 cut(s) | 79, 1582, 2726, 3847, 3930 |
| BshNI | GGYRCC | 3 cut(s) | 302, 366, 434 |
| BshTI | ACCGGT | 1 cut(s) | 413 |
| BshVI | ATCGAT | 1 cut(s) | 98 |
| BsiEI | CGRYCG | 1 cut(s) | 30 |
| BsiHKAI | GWGCWC | 4 cut(s) | 1005, 2281, 2456, 3111 |
| BsiHKCI | CYCGRG | 4 cut(s) | 173, 585, 1682, 1708 |
| BsiSI | CCGG | 8 cut(s) | 76, 174, 306, 350, 414, 586, 3416, 3911 |
| BslFI | GGGAC | 8 cut(s) | 155, 713, 1271, 1355, 1796, 2257, 2455, 3998 |
| BslI | CCNNNNNNNGG | 6 cut(s) | 1072, 1367, 2152, 3007, 3593, 3704 |
| BsmAI | GTCTC | 3 cut(s) | 166, 2475, 2627 |
| BsmBI | CGTCTC | 1 cut(s) | 166 |
| BsmFI | GGGAC | 8 cut(s) | 155, 713, 1271, 1355, 1796, 2257, 2455, 3998 |
| BsmI | GAATGC | 2 cut(s) | 214, 2131 |
| BsnI | GGCC | 5 cut(s) | 79, 1582, 2726, 3847, 3930 |
| BsoBI | CYCGRG | 4 cut(s) | 173, 585, 1682, 1708 |
| Bsp1286I | GDGCHC | 6 cut(s) | 180, 369, 1005, 2281, 2456, 3111 |
| Bsp1720I | GCTNAGC | 1 cut(s) | 2127 |
| Bsp19I | CCATGG | 2 cut(s) | 240, 2146 |
| BspANI | GGCC | 5 cut(s) | 79, 1582, 2726, 3847, 3930 |
| BspCNI | CTCAG | 7 cut(s) | 991, 1657, 2119, 2655, 2791, 3221, 3280 |
| BspDI | ATCGAT | 1 cut(s) | 98 |
| BspHI | TCATGA | 2 cut(s) | 1512, 3970 |
| BspMAI | CTGCAG | 2 cut(s) | 48, 1458 |
| BspMI | ACCTGC | 4 cut(s) | 51, 502, 3325, 3695 |
| BspQI | GCTCTTC | 1 cut(s) | 44 |
| BspT107I | GGYRCC | 3 cut(s) | 302, 366, 434 |
| BsrDI | GCAATG | 5 cut(s) | 891, 1320, 1570, 3558, 3623 |
| BsrFI | RCCGGY | 2 cut(s) | 75, 413 |
| BsrI | ACTGG | 9 cut(s) | 285, 548, 584, 2107, 2166, 2399, 2415, 2563, 3543 |
| BssAI | RCCGGY | 2 cut(s) | 75, 413 |
| BssNI | GRCGYC | 2 cut(s) | 303, 435 |
| BssT1I | CCWWGG | 6 cut(s) | 240, 688, 803, 2146, 2540, 2727 |
| Bst2UI | CCWGG | 4 cut(s) | 56, 1917, 2043, 2389 |
| Bst4CI | ACNGT | 9 cut(s) | 700, 1778, 1958, 1986, 2578, 2605, 2771, 2776, 3527 |
| Bst6I | CTCTTC | 7 cut(s) | 44, 1004, 1878, 3080, 3195, 3643, 3776 |
| BstACI | GRCGYC | 2 cut(s) | 303, 435 |
| BstAPI | GCANNNNNTGC | 2 cut(s) | 2102, 2162 |
| BstBAI | YACGTR | 1 cut(s) | 1006 |
| BstC8I | GCNNGC | 7 cut(s) | 333, 491, 1326, 1396, 1723, 1848, 3467 |
| BstDSI | CCRYGG | 2 cut(s) | 240, 2146 |
| BstEII | GGTNACC | 1 cut(s) | 256 |
| BstF5I | GGATG | 6 cut(s) | 689, 813, 1240, 2338, 2460, 3571 |
| BstH2I | RGCGCY | 2 cut(s) | 306, 438 |
| BstHHI | GCGC | 3 cut(s) | 66, 305, 437 |
| BstMAI | GTCTC | 3 cut(s) | 166, 2475, 2627 |
| BstMCI | CGRYCG | 1 cut(s) | 30 |
| BstNI | CCWGG | 4 cut(s) | 56, 1917, 2043, 2389 |
| BstNSI | RCATGY | 1 cut(s) | 2881 |
| BstPI | GGTNACC | 1 cut(s) | 256 |
| BstSFI | CTRYAG | 3 cut(s) | 44, 1454, 2775 |
| BstSLI | GKGCMC | 1 cut(s) | 369 |
| BstV2I | GAAGAC | 5 cut(s) | 121, 413, 1163, 1202, 3592 |
| BstX2I | RGATCY | 5 cut(s) | 232, 1999, 2536, 2731, 3382 |
| BstXI | CCANNNNNNTGG | 1 cut(s) | 2114 |
| BstYI | RGATCY | 5 cut(s) | 232, 1999, 2536, 2731, 3382 |
| Bsu15I | ATCGAT | 1 cut(s) | 98 |
| Bsu36I | CCTNAGG | 1 cut(s) | 2799 |
| BsuRI | GGCC | 5 cut(s) | 79, 1582, 2726, 3847, 3930 |
| BsuTUI | ATCGAT | 1 cut(s) | 98 |
| BtgI | CCRYGG | 2 cut(s) | 240, 2146 |
| BtgZI | GCGATG | 1 cut(s) | 137 |
| BtsCI | GGATG | 6 cut(s) | 689, 813, 1240, 2338, 2460, 3571 |
| BtsIMutI | CAGTG | 4 cut(s) | 292, 859, 1963, 2408 |
| BveI | ACCTGC | 4 cut(s) | 51, 502, 3325, 3695 |
| Cac8I | GCNNGC | 7 cut(s) | 333, 491, 1326, 1396, 1723, 1848, 3467 |
| CaiI | CAGNNNCTG | 1 cut(s) | 121 |
| CciI | TCATGA | 2 cut(s) | 1512, 3970 |
| CfoI | GCGC | 3 cut(s) | 66, 305, 437 |
| Cfr10I | RCCGGY | 2 cut(s) | 75, 413 |
| Cfr13I | GGNCC | 9 cut(s) | 78, 148, 582, 727, 1342, 1581, 1731, 2673, 3788 |
| Cfr9I | CCCGGG | 2 cut(s) | 173, 585 |
| ClaI | ATCGAT | 1 cut(s) | 98 |
| CseI | GACGC | 1 cut(s) | 3887 |
| CsiI | ACCWGGT | 1 cut(s) | 2387 |
| CspAI | ACCGGT | 1 cut(s) | 413 |
| CspCI | CAANNNNNGTGG | 4 cut(s) | 1113, 1148, 3135, 3170 |
| DinI | GGCGCC | 2 cut(s) | 304, 436 |
| DraI | TTTAAA | 1 cut(s) | 1621 |
| DrdI | GACNNNNNNGTC | 1 cut(s) | 146 |
| DseDI | GACNNNNNNGTC | 1 cut(s) | 146 |
| Eam1104I | CTCTTC | 7 cut(s) | 44, 1004, 1878, 3080, 3195, 3643, 3776 |
| EarI | CTCTTC | 7 cut(s) | 44, 1004, 1878, 3080, 3195, 3643, 3776 |
| EciI | GGCGGA | 1 cut(s) | 2012 |
| Ecl136II | GAGCTC | 2 cut(s) | 2454, 3109 |
| Eco130I | CCWWGG | 6 cut(s) | 240, 688, 803, 2146, 2540, 2727 |
| Eco24I | GRGCYC | 3 cut(s) | 180, 2456, 3111 |
| Eco32I | GATATC | 1 cut(s) | 540 |
| Eco47I | GGWCC | 7 cut(s) | 148, 582, 727, 1342, 1731, 2673, 3788 |
| Eco53kI | GAGCTC | 2 cut(s) | 2454, 3109 |
| Eco57I | CTGAAG | 3 cut(s) | 3201, 3905, 3909 |
| Eco72I | CACGTG | 1 cut(s) | 1006 |
| Eco81I | CCTNAGG | 1 cut(s) | 2799 |
| Eco88I | CYCGRG | 4 cut(s) | 173, 585, 1682, 1708 |
| Eco91I | GGTNACC | 1 cut(s) | 256 |
| EcoICRI | GAGCTC | 2 cut(s) | 2454, 3109 |
| EcoO109I | RGGNCCY | 1 cut(s) | 727 |
| EcoO65I | GGTNACC | 1 cut(s) | 256 |
| EcoRI | GAATTC | 2 cut(s) | 2942, 2963 |
| EcoRII | CCWGG | 4 cut(s) | 54, 1915, 2041, 2387 |
| EcoRV | GATATC | 1 cut(s) | 540 |
| EcoT14I | CCWWGG | 6 cut(s) | 240, 688, 803, 2146, 2540, 2727 |
| EcoT38I | GRGCYC | 3 cut(s) | 180, 2456, 3111 |
| EgeI | GGCGCC | 2 cut(s) | 304, 436 |
| EheI | GGCGCC | 2 cut(s) | 304, 436 |
| ErhI | CCWWGG | 6 cut(s) | 240, 688, 803, 2146, 2540, 2727 |
| Esp3I | CGTCTC | 1 cut(s) | 166 |
| FalI | AAGNNNNNCTT | 8 cut(s) | 1064, 1096, 1259, 1291, 1802, 1834, 2066, 2098 |
| FaqI | GGGAC | 8 cut(s) | 155, 713, 1271, 1355, 1796, 2257, 2455, 3998 |
| FauI | CCCGC | 2 cut(s) | 324, 3706 |
| FbaI | TGATCA | 3 cut(s) | 1509, 1519, 1930 |
| FokI | GGATG | 6 cut(s) | 696, 820, 1247, 2345, 2447, 3558 |
| FriOI | GRGCYC | 3 cut(s) | 180, 2456, 3111 |
| FspBI | CTAG | 5 cut(s) | 786, 1244, 1799, 2786, 3798 |
| GlaI | GCGC | 3 cut(s) | 65, 304, 436 |
| GsaI | CCCAGC | 1 cut(s) | 1323 |
| GsuI | CTGGAG | 4 cut(s) | 1250, 2470, 2717, 2907 |
| HaeII | RGCGCY | 2 cut(s) | 306, 438 |
| HaeIII | GGCC | 5 cut(s) | 79, 1582, 2726, 3847, 3930 |
| HapII | CCGG | 8 cut(s) | 76, 174, 306, 350, 414, 586, 3416, 3911 |
| HgaI | GACGC | 1 cut(s) | 3887 |
| HhaI | GCGC | 3 cut(s) | 66, 305, 437 |
| Hin1I | GRCGYC | 2 cut(s) | 303, 435 |
| Hin6I | GCGC | 3 cut(s) | 64, 303, 435 |
| HinP1I | GCGC | 3 cut(s) | 64, 303, 435 |
| HindIII | AAGCTT | 4 cut(s) | 1692, 1943, 3566, 3836 |
| HpaII | CCGG | 8 cut(s) | 76, 174, 306, 350, 414, 586, 3416, 3911 |
| Hpy166II | GTNNAC | 6 cut(s) | 419, 1118, 1272, 1969, 2673, 2791 |
| Hpy8I | GTNNAC | 6 cut(s) | 419, 1118, 1272, 1969, 2673, 2791 |
| Hpy99I | CGWCG | 4 cut(s) | 143, 269, 320, 488 |
| HpyCH4III | ACNGT | 9 cut(s) | 700, 1778, 1958, 1986, 2578, 2605, 2771, 2776, 3527 |
| HpyCH4IV | ACGT | 5 cut(s) | 168, 267, 927, 1005, 3507 |
| HpySE526I | ACGT | 5 cut(s) | 168, 267, 927, 1005, 3507 |
| Hsp92I | GRCGYC | 2 cut(s) | 303, 435 |
| HspAI | GCGC | 3 cut(s) | 64, 303, 435 |
| KasI | GGCGCC | 2 cut(s) | 302, 434 |
| KflI | GGGWCCC | 1 cut(s) | 727 |
| Ksp22I | TGATCA | 3 cut(s) | 1509, 1519, 1930 |
| LguI | GCTCTTC | 1 cut(s) | 44 |
| LmnI | GCTCC | 9 cut(s) | 61, 161, 1541, 1975, 2451, 3114, 3157, 3412, 3734 |
| LweI | GCATC | 5 cut(s) | 674, 1225, 1510, 3379, 3885 |
| MabI | ACCWGGT | 1 cut(s) | 2387 |
| MaeI | CTAG | 5 cut(s) | 786, 1244, 1799, 2786, 3798 |
| MaeII | ACGT | 5 cut(s) | 168, 267, 927, 1005, 3507 |
| MaeIII | GTNAC | 8 cut(s) | 256, 589, 854, 928, 2204, 2249, 3906, 3964 |
| MfeI | CAATTG | 1 cut(s) | 1851 |
| MflI | RGATCY | 5 cut(s) | 232, 1999, 2536, 2731, 3382 |
| MhlI | GDGCHC | 6 cut(s) | 180, 369, 1005, 2281, 2456, 3111 |
| Mly113I | GGCGCC | 2 cut(s) | 303, 435 |
| MmeI | TCCRAC | 4 cut(s) | 2973, 2988, 3136, 3712 |
| MroXI | GAANNNNTTC | 5 cut(s) | 278, 1170, 2931, 2946, 3122 |
| MslI | CAYNNNNRTG | 5 cut(s) | 1350, 2148, 2180, 2274, 3576 |
| MspA1I | CMGCKG | 3 cut(s) | 331, 3692, 3755 |
| MspI | CCGG | 8 cut(s) | 76, 174, 306, 350, 414, 586, 3416, 3911 |
| MunI | CAATTG | 1 cut(s) | 1851 |
| Mva1269I | GAATGC | 2 cut(s) | 214, 2131 |
| MvaI | CCWGG | 4 cut(s) | 56, 1917, 2043, 2389 |
| NarI | GGCGCC | 2 cut(s) | 303, 435 |
| NciI | CCSGG | 7 cut(s) | 174, 175, 307, 586, 587, 3417, 3912 |
| NcoI | CCATGG | 2 cut(s) | 240, 2146 |
| NmeAIII | GCCGAG | 1 cut(s) | 2275 |
| NmuCI | GTSAC | 5 cut(s) | 256, 589, 854, 928, 3964 |
| NspI | RCATGY | 1 cut(s) | 2881 |
| OliI | CACNNNNGTG | 1 cut(s) | 2148 |
| PaeR7I | CTCGAG | 1 cut(s) | 1708 |
| PagI | TCATGA | 2 cut(s) | 1512, 3970 |
| PaqCI | CACCTGC | 1 cut(s) | 502 |
| PciSI | GCTCTTC | 1 cut(s) | 44 |
| PcsI | WCGNNNNNNNCGW | 2 cut(s) | 138, 480 |
| PctI | GAATGC | 2 cut(s) | 214, 2131 |
| PdmI | GAANNNNTTC | 5 cut(s) | 278, 1170, 2931, 2946, 3122 |
| PinAI | ACCGGT | 1 cut(s) | 413 |
| Ple19I | CGATCG | 1 cut(s) | 30 |
| PluTI | GGCGCC | 2 cut(s) | 306, 438 |
| PmaCI | CACGTG | 1 cut(s) | 1006 |
| PmlI | CACGTG | 1 cut(s) | 1006 |
| Ppu21I | YACGTR | 1 cut(s) | 1006 |
| PpuMI | RGGWCCY | 1 cut(s) | 727 |
| PshBI | ATTAAT | 1 cut(s) | 2214 |
| PsiI | TTATAA | 2 cut(s) | 2472, 2685 |
| Psp124BI | GAGCTC | 2 cut(s) | 2456, 3111 |
| Psp5II | RGGWCCY | 1 cut(s) | 727 |
| Psp6I | CCWGG | 4 cut(s) | 54, 1915, 2041, 2387 |
| PspCI | CACGTG | 1 cut(s) | 1006 |
| PspEI | GGTNACC | 1 cut(s) | 256 |
| PspFI | CCCAGC | 1 cut(s) | 1319 |
| PspGI | CCWGG | 4 cut(s) | 54, 1915, 2041, 2387 |
| PspPI | GGNCC | 9 cut(s) | 78, 148, 582, 727, 1342, 1581, 1731, 2673, 3788 |
| PspPPI | RGGWCCY | 1 cut(s) | 727 |
| PspXI | VCTCGAGB | 1 cut(s) | 1708 |
| PsrI | GAACNNNNNNTAC | 2 cut(s) | 3268, 3300 |
| PstI | CTGCAG | 2 cut(s) | 48, 1458 |
| PstNI | CAGNNNCTG | 1 cut(s) | 121 |
| PsuI | RGATCY | 5 cut(s) | 232, 1999, 2536, 2731, 3382 |
| PvuI | CGATCG | 1 cut(s) | 30 |
| PvuII | CAGCTG | 1 cut(s) | 3692 |
| RseI | CAYNNNNRTG | 5 cut(s) | 1350, 2148, 2180, 2274, 3576 |
| SacI | GAGCTC | 2 cut(s) | 2456, 3111 |
| SapI | GCTCTTC | 1 cut(s) | 44 |
| Sau96I | GGNCC | 9 cut(s) | 78, 148, 582, 727, 1342, 1581, 1731, 2673, 3788 |
| ScaI | AGTACT | 4 cut(s) | 1742, 1765, 2170, 2773 |
| SduI | GDGCHC | 6 cut(s) | 180, 369, 1005, 2281, 2456, 3111 |
| SexAI | ACCWGGT | 1 cut(s) | 2387 |
| SfaNI | GCATC | 5 cut(s) | 674, 1225, 1510, 3379, 3885 |
| SfcI | CTRYAG | 3 cut(s) | 44, 1454, 2775 |
| SfoI | GGCGCC | 2 cut(s) | 304, 436 |
| Sfr274I | CTCGAG | 1 cut(s) | 1708 |
| SgrAI | CRCCGGYG | 1 cut(s) | 413 |
| SinI | GGWCC | 7 cut(s) | 148, 582, 727, 1342, 1731, 2673, 3788 |
| SlaI | CTCGAG | 1 cut(s) | 1708 |
| SmaI | CCCGGG | 2 cut(s) | 175, 587 |
| SmiMI | CAYNNNNRTG | 5 cut(s) | 1350, 2148, 2180, 2274, 3576 |
| SmlI | CTYRAG | 9 cut(s) | 251, 373, 1708, 2936, 3002, 3104, 3305, 3407, 3810 |
| SmoI | CTYRAG | 9 cut(s) | 251, 373, 1708, 2936, 3002, 3104, 3305, 3407, 3810 |
| SspDI | GGCGCC | 2 cut(s) | 302, 434 |
| SspI | AATATT | 1 cut(s) | 1435 |
| SspMI | CTAG | 5 cut(s) | 786, 1244, 1799, 2786, 3798 |
| SstI | GAGCTC | 2 cut(s) | 2456, 3111 |
| StyI | CCWWGG | 6 cut(s) | 240, 688, 803, 2146, 2540, 2727 |
| TaaI | ACNGT | 9 cut(s) | 700, 1778, 1958, 1986, 2578, 2605, 2771, 2776, 3527 |
| TaiI | ACGT | 5 cut(s) | 171, 270, 930, 1008, 3510 |
| TatI | WGTACW | 5 cut(s) | 504, 1740, 1763, 2168, 2771 |
| TauI | GCSGC | 5 cut(s) | 215, 435, 1728, 3758, 3850 |
| TscAI | CASTG | 4 cut(s) | 292, 859, 1963, 2415 |
| TseFI | GTSAC | 5 cut(s) | 256, 589, 854, 928, 3964 |
| Tsp45I | GTSAC | 5 cut(s) | 256, 589, 854, 928, 3964 |
| TspGWI | ACGGA | 5 cut(s) | 148, 225, 241, 2654, 3130 |
| TspMI | CCCGGG | 2 cut(s) | 173, 585 |
| TspRI | CASTG | 4 cut(s) | 292, 859, 1963, 2415 |
| VpaK11BI | GGWCC | 7 cut(s) | 148, 582, 727, 1342, 1731, 2673, 3788 |
| VspI | ATTAAT | 1 cut(s) | 2214 |
| XapI | RAATTY | 9 cut(s) | 464, 614, 2646, 2690, 2781, 2843, 2931, 2942, 2963 |
| XbaI | TCTAGA | 2 cut(s) | 785, 1798 |
| XceI | RCATGY | 1 cut(s) | 2881 |
| XcmI | CCANNNNNNNNNTGG | 4 cut(s) | 2538, 2667, 3369, 3550 |
| XhoI | CTCGAG | 1 cut(s) | 1708 |
| XmaI | CCCGGG | 2 cut(s) | 173, 585 |
| XmnI | GAANNNNTTC | 5 cut(s) | 278, 1170, 2931, 2946, 3122 |
| XspI | CTAG | 5 cut(s) | 786, 1244, 1799, 2786, 3798 |
| ZrmI | AGTACT | 4 cut(s) | 1742, 1765, 2170, 2773 |