ATP-dependent serine protease that mediates the selective degradation of misfolded, unassembled or oxidatively damaged polypeptides as well as certain short-lived regulatory proteins in the mitochondrial matrix. May also have a chaperone function in the assembly of inner membrane protein complexes. Participates in the regulation of mitochondrial gene expression and in the maintenance of the integrity of the mitochondrial genome. Binds to mitochondrial DNA in a site-specific manner
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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AarI | CACCTGC | 2 cut(s) | 1940, 2069 |
| AasI | GACNNNNNNGTC | 1 cut(s) | 578 |
| Acc36I | ACCTGC | 3 cut(s) | 1940, 2069, 2272 |
| AccII | CGCG | 1 cut(s) | 2237 |
| AciI | CCGC | 9 cut(s) | 58, 218, 314, 323, 400, 1453, 1990, 2099, 2844 |
| AclI | AACGTT | 1 cut(s) | 892 |
| AcoI | YGGCCR | 1 cut(s) | 589 |
| AcsI | RAATTY | 4 cut(s) | 1284, 1337, 2349, 2674 |
| AcuI | CTGAAG | 3 cut(s) | 20, 26, 677 |
| AcvI | CACGTG | 2 cut(s) | 1442, 1865 |
| AcyI | GRCGYC | 1 cut(s) | 237 |
| AfaI | GTAC | 4 cut(s) | 1551, 1741, 2512, 2605 |
| AflIII | ACRYGT | 2 cut(s) | 183, 1862 |
| AhdI | GACNNNNNGTC | 1 cut(s) | 241 |
| AjiI | CACGTC | 2 cut(s) | 688, 2751 |
| AjnI | CCWGG | 4 cut(s) | 1235, 1402, 1537, 2254 |
| AjuI | GAANNNNNNNTTGG | 2 cut(s) | 941, 973 |
| AloI | GAACNNNNNNTCC | 2 cut(s) | 194, 226 |
| Alw26I | GTCTC | 6 cut(s) | 470, 564, 1046, 1394, 1836, 2519 |
| AlwNI | CAGNNNCTG | 2 cut(s) | 2126, 2294 |
| Ama87I | CYCGRG | 1 cut(s) | 62 |
| ApeKI | GCWGC | 5 cut(s) | 377, 827, 2021, 2174, 2867 |
| ApoI | RAATTY | 4 cut(s) | 1284, 1337, 2349, 2674 |
| AspLEI | GCGC | 1 cut(s) | 422 |
| AspS9I | GGNCC | 8 cut(s) | 40, 65, 276, 1397, 1621, 2072, 2706, 2723 |
| AsuC2I | CCSGG | 5 cut(s) | 63, 64, 274, 333, 2465 |
| AsuHPI | GGTGA | 4 cut(s) | 928, 1643, 2270, 2372 |
| AsuII | TTCGAA | 3 cut(s) | 170, 604, 2672 |
| AvaI | CYCGRG | 1 cut(s) | 62 |
| AvaII | GGWCC | 2 cut(s) | 1621, 2723 |
| BaeGI | GKGCMC | 2 cut(s) | 1279, 1447 |
| BalI | TGGCCA | 1 cut(s) | 591 |
| BamHI | GGATCC | 3 cut(s) | 361, 2558, 2829 |
| BbrPI | CACGTG | 2 cut(s) | 1442, 1865 |
| BbsI | GAAGAC | 3 cut(s) | 1862, 2425, 2894 |
| BbvI | GCAGC | 5 cut(s) | 389, 814, 2033, 2186, 2879 |
| BccI | CCATC | 7 cut(s) | 610, 660, 986, 1540, 2063, 2176, 2714 |
| BceAI | ACGGC | 1 cut(s) | 1331 |
| BcgI | CGANNNNNNTGC | 2 cut(s) | 2915, 2949 |
| BciT130I | CCWGG | 4 cut(s) | 1237, 1404, 1539, 2256 |
| BciVI | GTATCC | 1 cut(s) | 2095 |
| BclI | TGATCA | 2 cut(s) | 2455, 2745 |
| BcnI | CCSGG | 5 cut(s) | 63, 64, 274, 333, 2465 |
| BcoDI | GTCTC | 6 cut(s) | 470, 564, 1046, 1394, 1836, 2519 |
| BfaI | CTAG | 6 cut(s) | 443, 878, 1214, 1688, 1839, 2727 |
| BfmI | CTRYAG | 4 cut(s) | 2076, 2265, 2700, 2980 |
| BfoI | RGCGCY | 1 cut(s) | 423 |
| BfuAI | ACCTGC | 3 cut(s) | 1940, 2069, 2272 |
| BfuI | GTATCC | 1 cut(s) | 2095 |
| BglI | GCCNNNNNGGC | 1 cut(s) | 39 |
| BglII | AGATCT | 1 cut(s) | 1983 |
| BisI | GCNGC | 8 cut(s) | 219, 314, 378, 401, 828, 2022, 2175, 2868 |
| BlsI | GCNGC | 8 cut(s) | 220, 315, 379, 402, 829, 2023, 2176, 2869 |
| Bme1390I | CCNGG | 9 cut(s) | 63, 64, 274, 333, 1237, 1404, 1539, 2256, 2465 |
| Bme18I | GGWCC | 2 cut(s) | 1621, 2723 |
| BmeRI | GACNNNNNGTC | 1 cut(s) | 241 |
| BmeT110I | CYCGRG | 1 cut(s) | 62 |
| BmgBI | CACGTC | 2 cut(s) | 688, 2751 |
| BmgT120I | GGNCC | 8 cut(s) | 40, 65, 276, 1397, 1621, 2072, 2706, 2723 |
| BmiI | GGNNCC | 8 cut(s) | 363, 472, 1366, 1622, 1961, 2560, 2707, 2831 |
| BmrFI | CCNGG | 9 cut(s) | 63, 64, 274, 333, 1237, 1404, 1539, 2256, 2465 |
| BmrI | ACTGGG | 3 cut(s) | 450, 1052, 2832 |
| BmsI | GCATC | 9 cut(s) | 92, 570, 685, 976, 1083, 1519, 2033, 2320, 2915 |
| BmuI | ACTGGG | 3 cut(s) | 450, 1052, 2832 |
| BpiI | GAAGAC | 3 cut(s) | 1862, 2425, 2894 |
| BpmI | CTGGAG | 2 cut(s) | 1425, 2244 |
| Bpu10I | CCTNAGC | 1 cut(s) | 1668 |
| Bpu14I | TTCGAA | 3 cut(s) | 170, 604, 2672 |
| BpuEI | CTTGAG | 2 cut(s) | 416, 1356 |
| BpuMI | CCSGG | 5 cut(s) | 63, 64, 274, 333, 2465 |
| BsaAI | YACGTR | 5 cut(s) | 791, 1205, 1442, 1801, 1865 |
| BsaBI | GATNNNNATC | 2 cut(s) | 966, 1296 |
| BsaHI | GRCGYC | 1 cut(s) | 237 |
| BsaI | GGTCTC | 2 cut(s) | 564, 2519 |
| BsaXI | ACNNNNNCTCC | 4 cut(s) | 561, 591, 2217, 2247 |
| Bse118I | RCCGGY | 5 cut(s) | 67, 88, 416, 597, 1178 |
| Bse1I | ACTGG | 7 cut(s) | 456, 918, 1047, 1168, 1810, 2036, 2827 |
| Bse3DI | GCAATG | 2 cut(s) | 308, 2805 |
| Bse8I | GATNNNNATC | 2 cut(s) | 966, 1296 |
| BseBI | CCWGG | 4 cut(s) | 1237, 1404, 1539, 2256 |
| BseGI | GGATG | 4 cut(s) | 561, 967, 2335, 2725 |
| BseJI | GATNNNNATC | 2 cut(s) | 966, 1296 |
| BseMI | GCAATG | 2 cut(s) | 308, 2805 |
| BseMII | CTCAG | 6 cut(s) | 794, 1372, 1659, 2169, 2334, 2546 |
| BseNI | ACTGG | 7 cut(s) | 456, 918, 1047, 1168, 1810, 2036, 2827 |
| BseRI | GAGGAG | 4 cut(s) | 10, 13, 238, 2890 |
| BseSI | GKGCMC | 2 cut(s) | 1279, 1447 |
| BseXI | GCAGC | 5 cut(s) | 389, 814, 2033, 2186, 2879 |
| BseYI | CCCAGC | 1 cut(s) | 75 |
| BsgI | GTGCAG | 1 cut(s) | 1148 |
| Bsh1236I | CGCG | 1 cut(s) | 2237 |
| BsiHKCI | CYCGRG | 1 cut(s) | 62 |
| BslFI | GGGAC | 3 cut(s) | 460, 553, 1634 |
| BsmAI | GTCTC | 6 cut(s) | 470, 564, 1046, 1394, 1836, 2519 |
| BsmFI | GGGAC | 3 cut(s) | 460, 553, 1634 |
| BsmI | GAATGC | 1 cut(s) | 1878 |
| Bso31I | GGTCTC | 2 cut(s) | 564, 2519 |
| BsoBI | CYCGRG | 1 cut(s) | 62 |
| Bsp119I | TTCGAA | 3 cut(s) | 170, 604, 2672 |
| Bsp1286I | GDGCHC | 2 cut(s) | 1279, 1447 |
| Bsp1407I | TGTACA | 1 cut(s) | 1739 |
| Bsp19I | CCATGG | 1 cut(s) | 2499 |
| Bsp68I | TCGCGA | 1 cut(s) | 2237 |
| BspACI | CCGC | 9 cut(s) | 58, 218, 314, 323, 400, 1453, 1990, 2099, 2844 |
| BspCNI | CTCAG | 6 cut(s) | 793, 1371, 1660, 2170, 2335, 2545 |
| BspFNI | CGCG | 1 cut(s) | 2237 |
| BspHI | TCATGA | 1 cut(s) | 2200 |
| BspLI | GGNNCC | 8 cut(s) | 363, 472, 1366, 1622, 1961, 2560, 2707, 2831 |
| BspMAI | CTGCAG | 3 cut(s) | 2080, 2269, 2704 |
| BspMI | ACCTGC | 3 cut(s) | 1940, 2069, 2272 |
| BspQI | GCTCTTC | 2 cut(s) | 867, 1920 |
| BspT104I | TTCGAA | 3 cut(s) | 170, 604, 2672 |
| BspTNI | GGTCTC | 2 cut(s) | 564, 2519 |
| BsrDI | GCAATG | 2 cut(s) | 308, 2805 |
| BsrFI | RCCGGY | 5 cut(s) | 67, 88, 416, 597, 1178 |
| BsrGI | TGTACA | 1 cut(s) | 1739 |
| BsrI | ACTGG | 7 cut(s) | 456, 918, 1047, 1168, 1810, 2036, 2827 |
| BssAI | RCCGGY | 5 cut(s) | 67, 88, 416, 597, 1178 |
| BssNI | GRCGYC | 1 cut(s) | 237 |
| BssT1I | CCWWGG | 3 cut(s) | 565, 806, 2499 |
| Bst2UI | CCWGG | 4 cut(s) | 1237, 1404, 1539, 2256 |
| Bst4CI | ACNGT | 7 cut(s) | 295, 640, 1250, 2198, 2377, 2623, 2984 |
| Bst6I | CTCTTC | 2 cut(s) | 867, 1920 |
| BstACI | GRCGYC | 1 cut(s) | 237 |
| BstAUI | TGTACA | 1 cut(s) | 1739 |
| BstBAI | YACGTR | 5 cut(s) | 791, 1205, 1442, 1801, 1865 |
| BstBI | TTCGAA | 3 cut(s) | 170, 604, 2672 |
| BstDEI | CTNAG | 6 cut(s) | 780, 1358, 1668, 2178, 2343, 2532 |
| BstDSI | CCRYGG | 1 cut(s) | 2499 |
| BstENI | CCTNNNNNAGG | 2 cut(s) | 431, 1721 |
| BstF5I | GGATG | 4 cut(s) | 561, 967, 2335, 2725 |
| BstFNI | CGCG | 1 cut(s) | 2237 |
| BstH2I | RGCGCY | 1 cut(s) | 423 |
| BstHHI | GCGC | 1 cut(s) | 422 |
| BstMAI | GTCTC | 6 cut(s) | 470, 564, 1046, 1394, 1836, 2519 |
| BstNI | CCWGG | 4 cut(s) | 1237, 1404, 1539, 2256 |
| BstNSI | RCATGY | 2 cut(s) | 346, 1875 |
| BstSCI | CCNGG | 9 cut(s) | 61, 62, 272, 331, 1235, 1402, 1537, 2254, 2463 |
| BstSFI | CTRYAG | 4 cut(s) | 2076, 2265, 2700, 2980 |
| BstSLI | GKGCMC | 2 cut(s) | 1279, 1447 |
| BstSNI | TACGTA | 1 cut(s) | 1801 |
| BstUI | CGCG | 1 cut(s) | 2237 |
| BstV1I | GCAGC | 5 cut(s) | 389, 814, 2033, 2186, 2879 |
| BstV2I | GAAGAC | 3 cut(s) | 1862, 2425, 2894 |
| BstX2I | RGATCY | 5 cut(s) | 361, 1983, 2248, 2558, 2829 |
| BstYI | RGATCY | 5 cut(s) | 361, 1983, 2248, 2558, 2829 |
| BsuI | GTATCC | 1 cut(s) | 2095 |
| BtgI | CCRYGG | 1 cut(s) | 2499 |
| BtgZI | GCGATG | 1 cut(s) | 69 |
| BtrI | CACGTC | 2 cut(s) | 688, 2751 |
| BtsCI | GGATG | 4 cut(s) | 561, 967, 2335, 2725 |
| BtsIMutI | CAGTG | 3 cut(s) | 1255, 1815, 3013 |
| BtuMI | TCGCGA | 1 cut(s) | 2237 |
| BveI | ACCTGC | 3 cut(s) | 1940, 2069, 2272 |
| CaiI | CAGNNNCTG | 2 cut(s) | 2126, 2294 |
| CciI | TCATGA | 1 cut(s) | 2200 |
| CfoI | GCGC | 1 cut(s) | 422 |
| Cfr10I | RCCGGY | 5 cut(s) | 67, 88, 416, 597, 1178 |
| Cfr13I | GGNCC | 8 cut(s) | 40, 65, 276, 1397, 1621, 2072, 2706, 2723 |
| Cfr9I | CCCGGG | 1 cut(s) | 62 |
| CseI | GACGC | 3 cut(s) | 245, 550, 1877 |
| CsiI | ACCWGGT | 1 cut(s) | 2254 |
| Csp6I | GTAC | 4 cut(s) | 1550, 1740, 2511, 2604 |
| CspCI | CAANNNNNGTGG | 2 cut(s) | 2518, 2553 |
| CviQI | GTAC | 4 cut(s) | 1550, 1740, 2511, 2604 |
| DdeI | CTNAG | 6 cut(s) | 780, 1358, 1668, 2178, 2343, 2532 |
| DraI | TTTAAA | 1 cut(s) | 897 |
| DrdI | GACNNNNNNGTC | 1 cut(s) | 578 |
| DriI | GACNNNNNGTC | 1 cut(s) | 241 |
| DseDI | GACNNNNNNGTC | 1 cut(s) | 578 |
| EaeI | YGGCCR | 1 cut(s) | 589 |
| Eam1104I | CTCTTC | 2 cut(s) | 867, 1920 |
| Eam1105I | GACNNNNNGTC | 1 cut(s) | 241 |
| EarI | CTCTTC | 2 cut(s) | 867, 1920 |
| EciI | GGCGGA | 1 cut(s) | 47 |
| Eco105I | TACGTA | 1 cut(s) | 1801 |
| Eco130I | CCWWGG | 3 cut(s) | 565, 806, 2499 |
| Eco31I | GGTCTC | 2 cut(s) | 564, 2519 |
| Eco47I | GGWCC | 2 cut(s) | 1621, 2723 |
| Eco57I | CTGAAG | 3 cut(s) | 20, 26, 677 |
| Eco72I | CACGTG | 2 cut(s) | 1442, 1865 |
| Eco88I | CYCGRG | 1 cut(s) | 62 |
| EcoNI | CCTNNNNNAGG | 2 cut(s) | 431, 1721 |
| EcoRI | GAATTC | 2 cut(s) | 2349, 2674 |
| EcoRII | CCWGG | 4 cut(s) | 1235, 1402, 1537, 2254 |
| EcoT14I | CCWWGG | 3 cut(s) | 565, 806, 2499 |
| ErhI | CCWWGG | 3 cut(s) | 565, 806, 2499 |
| FalI | AAGNNNNNCTT | 8 cut(s) | 273, 305, 567, 599, 852, 884, 2940, 2972 |
| FaqI | GGGAC | 3 cut(s) | 460, 553, 1634 |
| FauI | CCCGC | 1 cut(s) | 2837 |
| FauNDI | CATATG | 1 cut(s) | 412 |
| FbaI | TGATCA | 2 cut(s) | 2455, 2745 |
| Fnu4HI | GCNGC | 8 cut(s) | 219, 314, 378, 401, 828, 2022, 2175, 2868 |
| FokI | GGATG | 4 cut(s) | 548, 974, 2342, 2732 |
| FseI | GGCCGGCC | 1 cut(s) | 71 |
| Fsp4HI | GCNGC | 8 cut(s) | 219, 314, 378, 401, 828, 2022, 2175, 2868 |
| FspBI | CTAG | 6 cut(s) | 443, 878, 1214, 1688, 1839, 2727 |
| GlaI | GCGC | 1 cut(s) | 421 |
| GluI | GCNGC | 8 cut(s) | 219, 314, 378, 401, 828, 2022, 2175, 2868 |
| GsaI | CCCAGC | 1 cut(s) | 79 |
| GsuI | CTGGAG | 2 cut(s) | 1425, 2244 |
| HaeII | RGCGCY | 1 cut(s) | 423 |
| HgaI | GACGC | 3 cut(s) | 245, 550, 1877 |
| HhaI | GCGC | 1 cut(s) | 422 |
| Hin1I | GRCGYC | 1 cut(s) | 237 |
| Hin6I | GCGC | 1 cut(s) | 420 |
| HinP1I | GCGC | 1 cut(s) | 420 |
| HincII | GTYRAC | 4 cut(s) | 649, 1224, 2395, 2579 |
| HindII | GTYRAC | 4 cut(s) | 649, 1224, 2395, 2579 |
| HindIII | AAGCTT | 3 cut(s) | 8, 2681, 2930 |
| HinfI | GANTC | 9 cut(s) | 45, 124, 268, 943, 2232, 2239, 2309, 2396, 2448 |
| HphI | GGTGA | 4 cut(s) | 928, 1643, 2270, 2372 |
| Hpy166II | GTNNAC | 9 cut(s) | 49, 264, 649, 1016, 1224, 2261, 2395, 2579, 2965 |
| Hpy8I | GTNNAC | 9 cut(s) | 49, 264, 649, 1016, 1224, 2261, 2395, 2579, 2965 |
| Hpy99I | CGWCG | 2 cut(s) | 239, 1518 |
| HpyCH4III | ACNGT | 7 cut(s) | 295, 640, 1250, 2198, 2377, 2623, 2984 |
| HpyF3I | CTNAG | 6 cut(s) | 780, 1358, 1668, 2178, 2343, 2532 |
| Hsp92I | GRCGYC | 1 cut(s) | 237 |
| HspAI | GCGC | 1 cut(s) | 420 |
| KroI | GCCGGC | 3 cut(s) | 67, 416, 597 |
| KroNI | GCCGGC | 3 cut(s) | 69, 418, 599 |
| Ksp22I | TGATCA | 2 cut(s) | 2455, 2745 |
| LguI | GCTCTTC | 2 cut(s) | 867, 1920 |
| LmnI | GCTCC | 4 cut(s) | 412, 824, 1654, 2877 |
| Lsp1109I | GCAGC | 5 cut(s) | 389, 814, 2033, 2186, 2879 |
| LweI | GCATC | 9 cut(s) | 92, 570, 685, 976, 1083, 1519, 2033, 2320, 2915 |
| MabI | ACCWGGT | 1 cut(s) | 2254 |
| MaeI | CTAG | 6 cut(s) | 443, 878, 1214, 1688, 1839, 2727 |
| MaeIII | GTNAC | 6 cut(s) | 1801, 1865, 1900, 2192, 2569, 2812 |
| MfeI | CAATTG | 3 cut(s) | 751, 1434, 2838 |
| MflI | RGATCY | 5 cut(s) | 361, 1983, 2248, 2558, 2829 |
| MhlI | GDGCHC | 2 cut(s) | 1279, 1447 |
| MlsI | TGGCCA | 1 cut(s) | 591 |
| MluNI | TGGCCA | 1 cut(s) | 591 |
| MlyI | GAGTC | 4 cut(s) | 54, 118, 2241, 2390 |
| MmeI | TCCRAC | 7 cut(s) | 939, 1152, 1330, 1632, 2029, 2401, 2449 |
| Mox20I | TGGCCA | 1 cut(s) | 591 |
| MroNI | GCCGGC | 3 cut(s) | 67, 416, 597 |
| MscI | TGGCCA | 1 cut(s) | 591 |
| MslI | CAYNNNNRTG | 3 cut(s) | 1629, 2691, 2753 |
| Msp20I | TGGCCA | 1 cut(s) | 591 |
| MspA1I | CMGCKG | 3 cut(s) | 79, 325, 2177 |
| MspR9I | CCNGG | 9 cut(s) | 63, 64, 274, 333, 1237, 1404, 1539, 2256, 2465 |
| MunI | CAATTG | 3 cut(s) | 751, 1434, 2838 |
| Mva1269I | GAATGC | 1 cut(s) | 1878 |
| MvaI | CCWGG | 4 cut(s) | 1237, 1404, 1539, 2256 |
| MvnI | CGCG | 1 cut(s) | 2237 |
| NaeI | GCCGGC | 3 cut(s) | 69, 418, 599 |
| NciI | CCSGG | 5 cut(s) | 63, 64, 274, 333, 2465 |
| NcoI | CCATGG | 1 cut(s) | 2499 |
| NdeI | CATATG | 1 cut(s) | 412 |
| NgoMIV | GCCGGC | 3 cut(s) | 67, 416, 597 |
| NlaIV | GGNNCC | 8 cut(s) | 363, 472, 1366, 1622, 1961, 2560, 2707, 2831 |
| NmeAIII | GCCGAG | 6 cut(s) | 68, 84, 106, 125, 179, 1967 |
| NmuCI | GTSAC | 3 cut(s) | 1865, 1900, 2569 |
| NruI | TCGCGA | 1 cut(s) | 2237 |
| NspI | RCATGY | 2 cut(s) | 346, 1875 |
| NspV | TTCGAA | 3 cut(s) | 170, 604, 2672 |
| PagI | TCATGA | 1 cut(s) | 2200 |
| PaqCI | CACCTGC | 2 cut(s) | 1940, 2069 |
| PasI | CCCWGGG | 1 cut(s) | 1236 |
| PciSI | GCTCTTC | 2 cut(s) | 867, 1920 |
| PcsI | WCGNNNNNNNCGW | 1 cut(s) | 1710 |
| PctI | GAATGC | 1 cut(s) | 1878 |
| PdiI | GCCGGC | 3 cut(s) | 69, 418, 599 |
| PfeI | GAWTC | 5 cut(s) | 268, 943, 2239, 2309, 2448 |
| PkrI | GCNGC | 8 cut(s) | 220, 315, 379, 402, 829, 2023, 2176, 2869 |
| PleI | GAGTC | 4 cut(s) | 53, 118, 2240, 2390 |
| PmaCI | CACGTG | 2 cut(s) | 1442, 1865 |
| PmlI | CACGTG | 2 cut(s) | 1442, 1865 |
| PpsI | GAGTC | 4 cut(s) | 53, 118, 2240, 2390 |
| Ppu21I | YACGTR | 5 cut(s) | 791, 1205, 1442, 1801, 1865 |
| Psp1406I | AACGTT | 1 cut(s) | 892 |
| Psp6I | CCWGG | 4 cut(s) | 1235, 1402, 1537, 2254 |
| PspCI | CACGTG | 2 cut(s) | 1442, 1865 |
| PspFI | CCCAGC | 1 cut(s) | 75 |
| PspGI | CCWGG | 4 cut(s) | 1235, 1402, 1537, 2254 |
| PspN4I | GGNNCC | 8 cut(s) | 363, 472, 1366, 1622, 1961, 2560, 2707, 2831 |
| PspPI | GGNCC | 8 cut(s) | 40, 65, 276, 1397, 1621, 2072, 2706, 2723 |
| PstI | CTGCAG | 3 cut(s) | 2080, 2269, 2704 |
| PstNI | CAGNNNCTG | 2 cut(s) | 2126, 2294 |
| PsuI | RGATCY | 5 cut(s) | 361, 1983, 2248, 2558, 2829 |
| PvuII | CAGCTG | 2 cut(s) | 79, 2177 |
| RigI | GGCCGGCC | 1 cut(s) | 71 |
| RruI | TCGCGA | 1 cut(s) | 2237 |
| RsaI | GTAC | 4 cut(s) | 1551, 1741, 2512, 2605 |
| RsaNI | GTAC | 4 cut(s) | 1550, 1740, 2511, 2604 |
| RseI | CAYNNNNRTG | 3 cut(s) | 1629, 2691, 2753 |
| SapI | GCTCTTC | 2 cut(s) | 867, 1920 |
| SatI | GCNGC | 8 cut(s) | 219, 314, 378, 401, 828, 2022, 2175, 2868 |
| Sau96I | GGNCC | 8 cut(s) | 40, 65, 276, 1397, 1621, 2072, 2706, 2723 |
| SbfI | CCTGCAGG | 2 cut(s) | 2080, 2704 |
| SchI | GAGTC | 4 cut(s) | 54, 118, 2241, 2390 |
| ScrFI | CCNGG | 9 cut(s) | 63, 64, 274, 333, 1237, 1404, 1539, 2256, 2465 |
| SdaI | CCTGCAGG | 2 cut(s) | 2080, 2704 |
| SduI | GDGCHC | 2 cut(s) | 1279, 1447 |
| SexAI | ACCWGGT | 1 cut(s) | 2254 |
| SfaNI | GCATC | 9 cut(s) | 92, 570, 685, 976, 1083, 1519, 2033, 2320, 2915 |
| SfcI | CTRYAG | 4 cut(s) | 2076, 2265, 2700, 2980 |
| SfuI | TTCGAA | 3 cut(s) | 170, 604, 2672 |
| SinI | GGWCC | 2 cut(s) | 1621, 2723 |
| SmaI | CCCGGG | 1 cut(s) | 64 |
| SmiMI | CAYNNNNRTG | 3 cut(s) | 1629, 2691, 2753 |
| SmlI | CTYRAG | 2 cut(s) | 431, 1371 |
| SmoI | CTYRAG | 2 cut(s) | 431, 1371 |
| SnaBI | TACGTA | 1 cut(s) | 1801 |
| Sse8387I | CCTGCAGG | 2 cut(s) | 2080, 2704 |
| SsiI | CCGC | 9 cut(s) | 58, 218, 314, 323, 400, 1453, 1990, 2099, 2844 |
| SspI | AATATT | 1 cut(s) | 802 |
| SspMI | CTAG | 6 cut(s) | 443, 878, 1214, 1688, 1839, 2727 |
| StyD4I | CCNGG | 9 cut(s) | 61, 62, 272, 331, 1235, 1402, 1537, 2254, 2463 |
| StyI | CCWWGG | 3 cut(s) | 565, 806, 2499 |
| TaaI | ACNGT | 7 cut(s) | 295, 640, 1250, 2198, 2377, 2623, 2984 |
| TaqI | TCGA | 9 cut(s) | 170, 523, 604, 1516, 1713, 2402, 2643, 2672, 2925 |
| TatI | WGTACW | 1 cut(s) | 1739 |
| TauI | GCSGC | 3 cut(s) | 221, 316, 403 |
| TfiI | GAWTC | 5 cut(s) | 268, 943, 2239, 2309, 2448 |
| TscAI | CASTG | 3 cut(s) | 1255, 1822, 3013 |
| TseFI | GTSAC | 3 cut(s) | 1865, 1900, 2569 |
| TseI | GCWGC | 5 cut(s) | 377, 827, 2021, 2174, 2867 |
| Tsp45I | GTSAC | 3 cut(s) | 1865, 1900, 2569 |
| TspGWI | ACGGA | 2 cut(s) | 2261, 2752 |
| TspMI | CCCGGG | 1 cut(s) | 62 |
| TspRI | CASTG | 3 cut(s) | 1255, 1822, 3013 |
| VpaK11BI | GGWCC | 2 cut(s) | 1621, 2723 |
| XagI | CCTNNNNNAGG | 2 cut(s) | 431, 1721 |
| XapI | RAATTY | 4 cut(s) | 1284, 1337, 2349, 2674 |
| XbaI | TCTAGA | 1 cut(s) | 1687 |
| XceI | RCATGY | 2 cut(s) | 346, 1875 |
| XmaI | CCCGGG | 1 cut(s) | 62 |
| XspI | CTAG | 6 cut(s) | 443, 878, 1214, 1688, 1839, 2727 |