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
Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.
| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AanI | TTATAA | 1 cut(s) | 903 |
| Acc36I | ACCTGC | 2 cut(s) | 2056, 2233 |
| AccB7I | CCANNNNNTGG | 3 cut(s) | 431, 1248, 2669 |
| AccBSI | CCGCTC | 2 cut(s) | 340, 842 |
| AccII | CGCG | 1 cut(s) | 1216 |
| AclI | AACGTT | 1 cut(s) | 907 |
| AcoI | YGGCCR | 2 cut(s) | 157, 2962 |
| AcsI | RAATTY | 3 cut(s) | 1202, 1349, 2298 |
| AcuI | CTGAAG | 2 cut(s) | 26, 773 |
| AcvI | CACGTG | 2 cut(s) | 1454, 1877 |
| AfaI | GTAC | 6 cut(s) | 556, 1563, 1753, 2317, 2468, 2554 |
| AflIII | ACRYGT | 3 cut(s) | 1214, 1874, 2641 |
| AhdI | GACNNNNNGTC | 1 cut(s) | 2065 |
| AhlI | ACTAGT | 3 cut(s) | 758, 928, 2075 |
| AjnI | CCWGG | 6 cut(s) | 36, 346, 457, 1414, 1549, 2101 |
| AjuI | GAANNNNNNNTTGG | 2 cut(s) | 1772, 1804 |
| Alw21I | GWGCWC | 1 cut(s) | 96 |
| AlwNI | CAGNNNCTG | 4 cut(s) | 464, 488, 2057, 2255 |
| Ama87I | CYCGRG | 1 cut(s) | 80 |
| AoxI | GGCC | 9 cut(s) | 40, 83, 143, 157, 243, 2139, 2509, 2655, 2962 |
| ApaI | GGGCCC | 1 cut(s) | 87 |
| ApeKI | GCWGC | 6 cut(s) | 392, 1030, 1177, 1922, 2816, 2855 |
| ApoI | RAATTY | 3 cut(s) | 1202, 1349, 2298 |
| ArsI | GACNNNNNNTTYG | 2 cut(s) | 248, 280 |
| AspA2I | CCTAGG | 1 cut(s) | 55 |
| AsuC2I | CCSGG | 3 cut(s) | 81, 82, 133 |
| AsuHPI | GGTGA | 6 cut(s) | 121, 818, 1013, 1655, 2246, 2969 |
| AsuII | TTCGAA | 1 cut(s) | 619 |
| AvaI | CYCGRG | 1 cut(s) | 80 |
| AvaII | GGWCC | 5 cut(s) | 59, 1409, 1530, 2179, 2672 |
| AvrII | CCTAGG | 1 cut(s) | 55 |
| BaeGI | GKGCMC | 2 cut(s) | 87, 279 |
| BalI | TGGCCA | 1 cut(s) | 2964 |
| BamHI | GGATCC | 2 cut(s) | 376, 643 |
| BanII | GRGCYC | 4 cut(s) | 75, 87, 96, 1291 |
| BbrPI | CACGTG | 2 cut(s) | 1454, 1877 |
| BbsI | GAAGAC | 4 cut(s) | 9, 761, 1874, 2843 |
| Bbv12I | GWGCWC | 1 cut(s) | 96 |
| BbvI | GCAGC | 6 cut(s) | 404, 1042, 1189, 1934, 2828, 2867 |
| BccI | CCATC | 7 cut(s) | 182, 625, 675, 1552, 2422, 2663, 2954 |
| BceAI | ACGGC | 3 cut(s) | 88, 431, 1938 |
| BcgI | CGANNNNNNTGC | 2 cut(s) | 2864, 2898 |
| BciT130I | CCWGG | 6 cut(s) | 38, 348, 459, 1416, 1551, 2103 |
| BclI | TGATCA | 2 cut(s) | 196, 2404 |
| BcnI | CCSGG | 3 cut(s) | 81, 82, 133 |
| BcuI | ACTAGT | 3 cut(s) | 758, 928, 2075 |
| BfmI | CTRYAG | 5 cut(s) | 1175, 2049, 2226, 2811, 2853 |
| BfuAI | ACCTGC | 2 cut(s) | 2056, 2233 |
| BglI | GCCNNNNNGGC | 1 cut(s) | 39 |
| BglII | AGATCT | 1 cut(s) | 1995 |
| BlnI | CCTAGG | 1 cut(s) | 55 |
| Bme1390I | CCNGG | 9 cut(s) | 38, 81, 82, 133, 348, 459, 1416, 1551, 2103 |
| Bme18I | GGWCC | 5 cut(s) | 59, 1409, 1530, 2179, 2672 |
| BmeRI | GACNNNNNGTC | 1 cut(s) | 2065 |
| BmeT110I | CYCGRG | 1 cut(s) | 80 |
| BmiI | GGNNCC | 7 cut(s) | 74, 85, 378, 645, 1973, 2458, 2656 |
| BmrFI | CCNGG | 9 cut(s) | 38, 81, 82, 133, 348, 459, 1416, 1551, 2103 |
| BmrI | ACTGGG | 3 cut(s) | 1064, 2087, 2781 |
| BmsI | GCATC | 4 cut(s) | 340, 1531, 2045, 2269 |
| BmuI | ACTGGG | 3 cut(s) | 1064, 2087, 2781 |
| BpiI | GAAGAC | 4 cut(s) | 9, 761, 1874, 2843 |
| BplI | GAGNNNNNCTC | 2 cut(s) | 83, 115 |
| BpmI | CTGGAG | 3 cut(s) | 20, 1437, 2124 |
| Bpu10I | CCTNAGC | 1 cut(s) | 2118 |
| Bpu14I | TTCGAA | 1 cut(s) | 619 |
| BpuEI | CTTGAG | 2 cut(s) | 431, 656 |
| BpuMI | CCSGG | 3 cut(s) | 81, 82, 133 |
| BsaAI | YACGTR | 2 cut(s) | 1454, 1877 |
| BsaBI | GATNNNNATC | 3 cut(s) | 947, 1308, 2598 |
| BsaI | GGTCTC | 4 cut(s) | 484, 579, 2123, 2468 |
| BsaJI | CCNNGG | 9 cut(s) | 37, 55, 80, 228, 347, 458, 821, 1247, 2448 |
| BsaWI | WCCGGW | 1 cut(s) | 2413 |
| BsaXI | ACNNNNNCTCC | 2 cut(s) | 576, 606 |
| Bse118I | RCCGGY | 1 cut(s) | 2753 |
| Bse1I | ACTGG | 6 cut(s) | 927, 1059, 1197, 2093, 2527, 2776 |
| Bse3DI | GCAATG | 6 cut(s) | 317, 323, 1845, 2614, 2712, 2754 |
| Bse8I | GATNNNNATC | 3 cut(s) | 947, 1308, 2598 |
| BseBI | CCWGG | 6 cut(s) | 38, 348, 459, 1416, 1551, 2103 |
| BseDI | CCNNGG | 9 cut(s) | 37, 55, 80, 228, 347, 458, 821, 1247, 2448 |
| BseGI | GGATG | 5 cut(s) | 457, 700, 2284, 2674, 2699 |
| BseJI | GATNNNNATC | 3 cut(s) | 947, 1308, 2598 |
| BseMI | GCAATG | 6 cut(s) | 317, 323, 1845, 2614, 2712, 2754 |
| BseMII | CTCAG | 6 cut(s) | 240, 495, 809, 2127, 2132, 2495 |
| BseNI | ACTGG | 6 cut(s) | 927, 1059, 1197, 2093, 2527, 2776 |
| BseRI | GAGGAG | 4 cut(s) | 16, 653, 2836, 2844 |
| BseSI | GKGCMC | 2 cut(s) | 87, 279 |
| BseXI | GCAGC | 6 cut(s) | 404, 1042, 1189, 1934, 2828, 2867 |
| BseYI | CCCAGC | 3 cut(s) | 1817, 2215, 2651 |
| Bsh1236I | CGCG | 1 cut(s) | 1216 |
| Bsh1285I | CGRYCG | 1 cut(s) | 338 |
| BshFI | GGCC | 9 cut(s) | 42, 85, 145, 159, 245, 2141, 2511, 2657, 2964 |
| BsiEI | CGRYCG | 1 cut(s) | 338 |
| BsiHKAI | GWGCWC | 1 cut(s) | 96 |
| BsiHKCI | CYCGRG | 1 cut(s) | 80 |
| BsiSI | CCGG | 4 cut(s) | 81, 132, 2414, 2754 |
| BslFI | GGGAC | 2 cut(s) | 63, 475 |
| BsmBI | CGTCTC | 2 cut(s) | 738, 2282 |
| BsmFI | GGGAC | 2 cut(s) | 63, 475 |
| BsmI | GAATGC | 1 cut(s) | 576 |
| BsnI | GGCC | 9 cut(s) | 42, 85, 145, 159, 245, 2141, 2511, 2657, 2964 |
| Bso31I | GGTCTC | 4 cut(s) | 484, 579, 2123, 2468 |
| BsoBI | CYCGRG | 1 cut(s) | 80 |
| Bsp119I | TTCGAA | 1 cut(s) | 619 |
| Bsp120I | GGGCCC | 1 cut(s) | 83 |
| Bsp1286I | GDGCHC | 5 cut(s) | 75, 87, 96, 279, 1291 |
| Bsp1407I | TGTACA | 2 cut(s) | 1751, 2466 |
| Bsp19I | CCATGG | 2 cut(s) | 1247, 2448 |
| BspANI | GGCC | 9 cut(s) | 42, 85, 145, 159, 245, 2141, 2511, 2657, 2964 |
| BspCNI | CTCAG | 6 cut(s) | 241, 494, 808, 2128, 2131, 2494 |
| BspFNI | CGCG | 1 cut(s) | 1216 |
| BspLI | GGNNCC | 7 cut(s) | 74, 85, 378, 645, 1973, 2458, 2656 |
| BspMAI | CTGCAG | 4 cut(s) | 1179, 2053, 2230, 2857 |
| BspMI | ACCTGC | 2 cut(s) | 2056, 2233 |
| BspQI | GCTCTTC | 3 cut(s) | 882, 1155, 1932 |
| BspT104I | TTCGAA | 1 cut(s) | 619 |
| BspTNI | GGTCTC | 4 cut(s) | 484, 579, 2123, 2468 |
| BsrBI | CCGCTC | 2 cut(s) | 340, 842 |
| BsrDI | GCAATG | 6 cut(s) | 317, 323, 1845, 2614, 2712, 2754 |
| BsrFI | RCCGGY | 1 cut(s) | 2753 |
| BsrGI | TGTACA | 2 cut(s) | 1751, 2466 |
| BsrI | ACTGG | 6 cut(s) | 927, 1059, 1197, 2093, 2527, 2776 |
| BssAI | RCCGGY | 1 cut(s) | 2753 |
| BssECI | CCNNGG | 9 cut(s) | 37, 55, 80, 228, 347, 458, 821, 1247, 2448 |
| BssT1I | CCWWGG | 4 cut(s) | 55, 821, 1247, 2448 |
| Bst2UI | CCWGG | 6 cut(s) | 38, 348, 459, 1416, 1551, 2103 |
| Bst4CI | ACNGT | 6 cut(s) | 310, 655, 1262, 1466, 2326, 2572 |
| Bst6I | CTCTTC | 4 cut(s) | 882, 981, 1155, 1932 |
| BstAPI | GCANNNNNTGC | 1 cut(s) | 1088 |
| BstAUI | TGTACA | 2 cut(s) | 1751, 2466 |
| BstBAI | YACGTR | 2 cut(s) | 1454, 1877 |
| BstBI | TTCGAA | 1 cut(s) | 619 |
| BstC8I | GCNNGC | 5 cut(s) | 96, 125, 420, 1638, 2883 |
| BstDEI | CTNAG | 8 cut(s) | 249, 381, 481, 795, 1370, 2118, 2136, 2481 |
| BstDSI | CCRYGG | 2 cut(s) | 1247, 2448 |
| BstENI | CCTNNNNNAGG | 2 cut(s) | 1733, 2229 |
| BstF5I | GGATG | 5 cut(s) | 457, 700, 2284, 2674, 2699 |
| BstFNI | CGCG | 1 cut(s) | 1216 |
| BstMCI | CGRYCG | 1 cut(s) | 338 |
| BstNI | CCWGG | 6 cut(s) | 38, 348, 459, 1416, 1551, 2103 |
| BstNSI | RCATGY | 5 cut(s) | 361, 422, 1640, 1887, 2645 |
| BstSCI | CCNGG | 9 cut(s) | 36, 79, 80, 131, 346, 457, 1414, 1549, 2101 |
| BstSFI | CTRYAG | 5 cut(s) | 1175, 2049, 2226, 2811, 2853 |
| BstSLI | GKGCMC | 2 cut(s) | 87, 279 |
| BstUI | CGCG | 1 cut(s) | 1216 |
| BstV1I | GCAGC | 6 cut(s) | 404, 1042, 1189, 1934, 2828, 2867 |
| BstV2I | GAAGAC | 4 cut(s) | 9, 761, 1874, 2843 |
| BstX2I | RGATCY | 6 cut(s) | 376, 643, 1995, 2209, 2599, 2778 |
| BstYI | RGATCY | 6 cut(s) | 376, 643, 1995, 2209, 2599, 2778 |
| BsuRI | GGCC | 9 cut(s) | 42, 85, 145, 159, 245, 2141, 2511, 2657, 2964 |
| BtgI | CCRYGG | 2 cut(s) | 1247, 2448 |
| BtsCI | GGATG | 5 cut(s) | 457, 700, 2284, 2674, 2699 |
| BtsIMutI | CAGTG | 3 cut(s) | 920, 1204, 1267 |
| BveI | ACCTGC | 2 cut(s) | 2056, 2233 |
| Cac8I | GCNNGC | 5 cut(s) | 96, 125, 420, 1638, 2883 |
| CaiI | CAGNNNCTG | 4 cut(s) | 464, 488, 2057, 2255 |
| Cfr10I | RCCGGY | 1 cut(s) | 2753 |
| Cfr9I | CCCGGG | 1 cut(s) | 80 |
| CseI | GACGC | 1 cut(s) | 1222 |
| Csp6I | GTAC | 6 cut(s) | 555, 1562, 1752, 2316, 2467, 2553 |
| CspCI | CAANNNNNGTGG | 4 cut(s) | 1746, 1781, 2467, 2502 |
| CviQI | GTAC | 6 cut(s) | 555, 1562, 1752, 2316, 2467, 2553 |
| DdeI | CTNAG | 8 cut(s) | 249, 381, 481, 795, 1370, 2118, 2136, 2481 |
| DraI | TTTAAA | 2 cut(s) | 912, 2274 |
| DriI | GACNNNNNGTC | 1 cut(s) | 2065 |
| EaeI | YGGCCR | 2 cut(s) | 157, 2962 |
| Eam1104I | CTCTTC | 4 cut(s) | 882, 981, 1155, 1932 |
| Eam1105I | GACNNNNNGTC | 1 cut(s) | 2065 |
| EarI | CTCTTC | 4 cut(s) | 882, 981, 1155, 1932 |
| EciI | GGCGGA | 1 cut(s) | 221 |
| Ecl136II | GAGCTC | 1 cut(s) | 94 |
| Eco130I | CCWWGG | 4 cut(s) | 55, 821, 1247, 2448 |
| Eco147I | AGGCCT | 1 cut(s) | 2511 |
| Eco24I | GRGCYC | 4 cut(s) | 75, 87, 96, 1291 |
| Eco31I | GGTCTC | 4 cut(s) | 484, 579, 2123, 2468 |
| Eco47I | GGWCC | 5 cut(s) | 59, 1409, 1530, 2179, 2672 |
| Eco53kI | GAGCTC | 1 cut(s) | 94 |
| Eco57I | CTGAAG | 2 cut(s) | 26, 773 |
| Eco72I | CACGTG | 2 cut(s) | 1454, 1877 |
| Eco88I | CYCGRG | 1 cut(s) | 80 |
| EcoICRI | GAGCTC | 1 cut(s) | 94 |
| EcoNI | CCTNNNNNAGG | 2 cut(s) | 1733, 2229 |
| EcoO109I | RGGNCCY | 1 cut(s) | 59 |
| EcoRII | CCWGG | 6 cut(s) | 36, 346, 457, 1414, 1549, 2101 |
| EcoT14I | CCWWGG | 4 cut(s) | 55, 821, 1247, 2448 |
| EcoT38I | GRGCYC | 4 cut(s) | 75, 87, 96, 1291 |
| ErhI | CCWWGG | 4 cut(s) | 55, 821, 1247, 2448 |
| Esp3I | CGTCTC | 2 cut(s) | 738, 2282 |
| FalI | AAGNNNNNCTT | 6 cut(s) | 1149, 1181, 2496, 2528, 2889, 2921 |
| FaqI | GGGAC | 2 cut(s) | 63, 475 |
| FauI | CCCGC | 2 cut(s) | 1657, 2786 |
| FauNDI | CATATG | 1 cut(s) | 427 |
| FbaI | TGATCA | 2 cut(s) | 196, 2404 |
| FokI | GGATG | 5 cut(s) | 464, 707, 2291, 2681, 2686 |
| FriOI | GRGCYC | 4 cut(s) | 75, 87, 96, 1291 |
| GsaI | CCCAGC | 3 cut(s) | 1821, 2219, 2655 |
| GsuI | CTGGAG | 3 cut(s) | 20, 1437, 2124 |
| HaeIII | GGCC | 9 cut(s) | 42, 85, 145, 159, 245, 2141, 2511, 2657, 2964 |
| HapII | CCGG | 4 cut(s) | 81, 132, 2414, 2754 |
| HgaI | GACGC | 1 cut(s) | 1222 |
| HincII | GTYRAC | 4 cut(s) | 138, 664, 1236, 2528 |
| HindII | GTYRAC | 4 cut(s) | 138, 664, 1236, 2528 |
| HindIII | AAGCTT | 3 cut(s) | 8, 914, 2630 |
| HpaII | CCGG | 4 cut(s) | 81, 132, 2414, 2754 |
| HphI | GGTGA | 6 cut(s) | 121, 818, 1013, 1655, 2246, 2969 |
| Hpy166II | GTNNAC | 8 cut(s) | 138, 664, 1004, 1236, 1412, 2179, 2528, 2914 |
| Hpy8I | GTNNAC | 8 cut(s) | 138, 664, 1004, 1236, 1412, 2179, 2528, 2914 |
| Hpy99I | CGWCG | 5 cut(s) | 268, 299, 721, 1530, 2879 |
| HpyCH4III | ACNGT | 6 cut(s) | 310, 655, 1262, 1466, 2326, 2572 |
| HpyCH4IV | ACGT | 6 cut(s) | 716, 747, 907, 1453, 1578, 1876 |
| HpyF3I | CTNAG | 8 cut(s) | 249, 381, 481, 795, 1370, 2118, 2136, 2481 |
| HpySE526I | ACGT | 6 cut(s) | 716, 747, 907, 1453, 1578, 1876 |
| Ksp22I | TGATCA | 2 cut(s) | 196, 2404 |
| LguI | GCTCTTC | 3 cut(s) | 882, 1155, 1932 |
| LmnI | GCTCC | 5 cut(s) | 78, 427, 839, 1666, 2033 |
| Lsp1109I | GCAGC | 6 cut(s) | 404, 1042, 1189, 1934, 2828, 2867 |
| LweI | GCATC | 4 cut(s) | 340, 1531, 2045, 2269 |
| MaeII | ACGT | 6 cut(s) | 716, 747, 907, 1453, 1578, 1876 |
| MaeIII | GTNAC | 4 cut(s) | 1210, 1380, 1912, 2761 |
| MbiI | CCGCTC | 2 cut(s) | 340, 842 |
| MfeI | CAATTG | 5 cut(s) | 270, 981, 1446, 1722, 2787 |
| MflI | RGATCY | 6 cut(s) | 376, 643, 1995, 2209, 2599, 2778 |
| MhlI | GDGCHC | 5 cut(s) | 75, 87, 96, 279, 1291 |
| MlsI | TGGCCA | 1 cut(s) | 2964 |
| MluI | ACGCGT | 1 cut(s) | 1214 |
| MluNI | TGGCCA | 1 cut(s) | 2964 |
| MlyI | GAGTC | 4 cut(s) | 133, 260, 285, 2404 |
| MmeI | TCCRAC | 3 cut(s) | 1508, 1644, 2398 |
| Mox20I | TGGCCA | 1 cut(s) | 2964 |
| MscI | TGGCCA | 1 cut(s) | 2964 |
| MslI | CAYNNNNRTG | 4 cut(s) | 804, 1641, 2640, 2717 |
| Msp20I | TGGCCA | 1 cut(s) | 2964 |
| MspA1I | CMGCKG | 1 cut(s) | 248 |
| MspI | CCGG | 4 cut(s) | 81, 132, 2414, 2754 |
| MspR9I | CCNGG | 9 cut(s) | 38, 81, 82, 133, 348, 459, 1416, 1551, 2103 |
| MunI | CAATTG | 5 cut(s) | 270, 981, 1446, 1722, 2787 |
| Mva1269I | GAATGC | 1 cut(s) | 576 |
| MvaI | CCWGG | 6 cut(s) | 38, 348, 459, 1416, 1551, 2103 |
| MvnI | CGCG | 1 cut(s) | 1216 |
| NciI | CCSGG | 3 cut(s) | 81, 82, 133 |
| NcoI | CCATGG | 2 cut(s) | 1247, 2448 |
| NdeI | CATATG | 1 cut(s) | 427 |
| NlaIV | GGNNCC | 7 cut(s) | 74, 85, 378, 645, 1973, 2458, 2656 |
| NmeAIII | GCCGAG | 3 cut(s) | 121, 185, 253 |
| NmuCI | GTSAC | 3 cut(s) | 1210, 1380, 1912 |
| NspI | RCATGY | 5 cut(s) | 361, 422, 1640, 1887, 2645 |
| NspV | TTCGAA | 1 cut(s) | 619 |
| PaeI | GCATGC | 2 cut(s) | 422, 1640 |
| PceI | AGGCCT | 1 cut(s) | 2511 |
| PciI | ACATGT | 1 cut(s) | 2641 |
| PciSI | GCTCTTC | 3 cut(s) | 882, 1155, 1932 |
| PcsI | WCGNNNNNNNCGW | 1 cut(s) | 260 |
| PctI | GAATGC | 1 cut(s) | 576 |
| PfeI | GAWTC | 8 cut(s) | 45, 958, 965, 1297, 1479, 1780, 2195, 2624 |
| PflMI | CCANNNNNTGG | 3 cut(s) | 431, 1248, 2669 |
| PleI | GAGTC | 4 cut(s) | 133, 259, 285, 2404 |
| PmaCI | CACGTG | 2 cut(s) | 1454, 1877 |
| PmlI | CACGTG | 2 cut(s) | 1454, 1877 |
| PpsI | GAGTC | 4 cut(s) | 133, 259, 285, 2404 |
| Ppu21I | YACGTR | 2 cut(s) | 1454, 1877 |
| PpuMI | RGGWCCY | 1 cut(s) | 59 |
| PscI | ACATGT | 1 cut(s) | 2641 |
| PsiI | TTATAA | 1 cut(s) | 903 |
| Psp124BI | GAGCTC | 1 cut(s) | 96 |
| Psp1406I | AACGTT | 1 cut(s) | 907 |
| Psp5II | RGGWCCY | 1 cut(s) | 59 |
| Psp6I | CCWGG | 6 cut(s) | 36, 346, 457, 1414, 1549, 2101 |
| PspCI | CACGTG | 2 cut(s) | 1454, 1877 |
| PspFI | CCCAGC | 3 cut(s) | 1817, 2215, 2651 |
| PspGI | CCWGG | 6 cut(s) | 36, 346, 457, 1414, 1549, 2101 |
| PspN4I | GGNNCC | 7 cut(s) | 74, 85, 378, 645, 1973, 2458, 2656 |
| PspOMI | GGGCCC | 1 cut(s) | 83 |
| PspPPI | RGGWCCY | 1 cut(s) | 59 |
| PstI | CTGCAG | 4 cut(s) | 1179, 2053, 2230, 2857 |
| PstNI | CAGNNNCTG | 4 cut(s) | 464, 488, 2057, 2255 |
| PsuI | RGATCY | 6 cut(s) | 376, 643, 1995, 2209, 2599, 2778 |
| RsaI | GTAC | 6 cut(s) | 556, 1563, 1753, 2317, 2468, 2554 |
| RsaNI | GTAC | 6 cut(s) | 555, 1562, 1752, 2316, 2467, 2553 |
| RseI | CAYNNNNRTG | 4 cut(s) | 804, 1641, 2640, 2717 |
| SacI | GAGCTC | 1 cut(s) | 96 |
| SapI | GCTCTTC | 3 cut(s) | 882, 1155, 1932 |
| SchI | GAGTC | 4 cut(s) | 133, 260, 285, 2404 |
| ScrFI | CCNGG | 9 cut(s) | 38, 81, 82, 133, 348, 459, 1416, 1551, 2103 |
| SduI | GDGCHC | 5 cut(s) | 75, 87, 96, 279, 1291 |
| SfaNI | GCATC | 4 cut(s) | 340, 1531, 2045, 2269 |
| SfcI | CTRYAG | 5 cut(s) | 1175, 2049, 2226, 2811, 2853 |
| SfuI | TTCGAA | 1 cut(s) | 619 |
| SinI | GGWCC | 5 cut(s) | 59, 1409, 1530, 2179, 2672 |
| SmaI | CCCGGG | 1 cut(s) | 82 |
| SmiMI | CAYNNNNRTG | 4 cut(s) | 804, 1641, 2640, 2717 |
| SmlI | CTYRAG | 2 cut(s) | 446, 671 |
| SmoI | CTYRAG | 2 cut(s) | 446, 671 |
| SpeI | ACTAGT | 3 cut(s) | 758, 928, 2075 |
| SphI | GCATGC | 2 cut(s) | 422, 1640 |
| SseBI | AGGCCT | 1 cut(s) | 2511 |
| SspI | AATATT | 1 cut(s) | 2847 |
| SstI | GAGCTC | 1 cut(s) | 96 |
| StuI | AGGCCT | 1 cut(s) | 2511 |
| StyD4I | CCNGG | 9 cut(s) | 36, 79, 80, 131, 346, 457, 1414, 1549, 2101 |
| StyI | CCWWGG | 4 cut(s) | 55, 821, 1247, 2448 |
| TaaI | ACNGT | 6 cut(s) | 310, 655, 1262, 1466, 2326, 2572 |
| TaiI | ACGT | 6 cut(s) | 719, 750, 910, 1456, 1581, 1879 |
| TaqI | TCGA | 9 cut(s) | 254, 294, 334, 619, 734, 2097, 2592, 2874, 2943 |
| TatI | WGTACW | 2 cut(s) | 1751, 2466 |
| TauI | GCSGC | 4 cut(s) | 248, 331, 845, 1014 |
| TfiI | GAWTC | 8 cut(s) | 45, 958, 965, 1297, 1479, 1780, 2195, 2624 |
| TscAI | CASTG | 3 cut(s) | 927, 1204, 1267 |
| TseFI | GTSAC | 3 cut(s) | 1210, 1380, 1912 |
| TseI | GCWGC | 6 cut(s) | 392, 1030, 1177, 1922, 2816, 2855 |
| Tsp45I | GTSAC | 3 cut(s) | 1210, 1380, 1912 |
| TspDTI | ATGAA | 9 cut(s) | 561, 1320, 1848, 2058, 2274, 2504, 2558, 2624, 2735 |
| TspGWI | ACGGA | 4 cut(s) | 65, 524, 2282, 2306 |
| TspMI | CCCGGG | 1 cut(s) | 80 |
| TspRI | CASTG | 3 cut(s) | 927, 1204, 1267 |
| Van91I | CCANNNNNTGG | 3 cut(s) | 431, 1248, 2669 |
| VpaK11BI | GGWCC | 5 cut(s) | 59, 1409, 1530, 2179, 2672 |
| XagI | CCTNNNNNAGG | 2 cut(s) | 1733, 2229 |
| XapI | RAATTY | 3 cut(s) | 1202, 1349, 2298 |
| XceI | RCATGY | 5 cut(s) | 361, 422, 1640, 1887, 2645 |
| XmaI | CCCGGG | 1 cut(s) | 80 |
| XmaJI | CCTAGG | 1 cut(s) | 55 |