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) |
|---|---|---|---|
| AanI | TTATAA | 2 cut(s) | 678, 894 |
| AarI | CACCTGC | 1 cut(s) | 89 |
| Acc36I | ACCTGC | 3 cut(s) | 89, 2047, 2104 |
| AccB1I | GGYRCC | 1 cut(s) | 425 |
| AccB7I | CCANNNNNTGG | 3 cut(s) | 55, 1239, 2675 |
| AccBSI | CCGCTC | 1 cut(s) | 331 |
| AccII | CGCG | 1 cut(s) | 1207 |
| AciI | CCGC | 8 cut(s) | 76, 206, 233, 329, 1003, 1993, 2042, 2799 |
| AclI | AACGTT | 1 cut(s) | 898 |
| AcoI | YGGCCR | 1 cut(s) | 157 |
| AcsI | RAATTY | 3 cut(s) | 1193, 1340, 2304 |
| AcuI | CTGAAG | 2 cut(s) | 26, 764 |
| AcvI | CACGTG | 2 cut(s) | 1445, 1868 |
| AfaI | GTAC | 4 cut(s) | 547, 1554, 1744, 2560 |
| AflIII | ACRYGT | 3 cut(s) | 1205, 1865, 2647 |
| AgeI | ACCGGT | 2 cut(s) | 2528, 2759 |
| AhlI | ACTAGT | 3 cut(s) | 749, 919, 2069 |
| AjnI | CCWGG | 9 cut(s) | 36, 54, 198, 337, 448, 1238, 1405, 1540, 2608 |
| AjuI | GAANNNNNNNTTGG | 2 cut(s) | 2220, 2252 |
| Alw21I | GWGCWC | 2 cut(s) | 96, 1158 |
| AlwNI | CAGNNNCTG | 1 cut(s) | 479 |
| AoxI | GGCC | 7 cut(s) | 40, 58, 143, 157, 237, 1179, 2661 |
| ApaI | GGGCCC | 2 cut(s) | 62, 147 |
| ApeKI | GCWGC | 9 cut(s) | 319, 383, 833, 997, 1021, 1168, 1913, 2822, 2861 |
| ApoI | RAATTY | 3 cut(s) | 1193, 1340, 2304 |
| ArsI | GACNNNNNNTTYG | 2 cut(s) | 2906, 2938 |
| AsiGI | ACCGGT | 2 cut(s) | 2528, 2759 |
| Asp700I | GAANNNNTTC | 1 cut(s) | 2148 |
| AspLEI | GCGC | 2 cut(s) | 1002, 1282 |
| AspS9I | GGNCC | 9 cut(s) | 40, 58, 59, 143, 144, 1400, 2185, 2661, 2678 |
| AsuC2I | CCSGG | 1 cut(s) | 133 |
| AsuHPI | GGTGA | 7 cut(s) | 121, 809, 1004, 1646, 2252, 2774, 2975 |
| AsuII | TTCGAA | 1 cut(s) | 610 |
| AsuNHI | GCTAGC | 1 cut(s) | 2177 |
| AvaII | GGWCC | 3 cut(s) | 1400, 2185, 2678 |
| BaeGI | GKGCMC | 3 cut(s) | 62, 147, 270 |
| BamHI | GGATCC | 2 cut(s) | 367, 634 |
| BanI | GGYRCC | 1 cut(s) | 425 |
| BanII | GRGCYC | 5 cut(s) | 62, 75, 96, 147, 1158 |
| BbrPI | CACGTG | 2 cut(s) | 1445, 1868 |
| BbsI | GAAGAC | 4 cut(s) | 752, 1865, 2510, 2849 |
| Bbv12I | GWGCWC | 2 cut(s) | 96, 1158 |
| BbvCI | CCTCAGC | 1 cut(s) | 228 |
| BbvI | GCAGC | 9 cut(s) | 306, 395, 820, 1009, 1033, 1180, 1925, 2834, 2873 |
| BccI | CCATC | 7 cut(s) | 182, 616, 666, 1543, 2428, 2669, 2855 |
| BceAI | ACGGC | 3 cut(s) | 88, 422, 1334 |
| BcgI | CGANNNNNNTGC | 2 cut(s) | 2870, 2904 |
| BciT130I | CCWGG | 9 cut(s) | 38, 56, 200, 339, 450, 1240, 1407, 1542, 2610 |
| BciVI | GTATCC | 1 cut(s) | 2278 |
| BclI | TGATCA | 1 cut(s) | 2410 |
| BcnI | CCSGG | 1 cut(s) | 133 |
| BcuI | ACTAGT | 3 cut(s) | 749, 919, 2069 |
| BfaI | CTAG | 9 cut(s) | 462, 750, 884, 920, 1217, 1842, 2070, 2178, 2682 |
| BfmI | CTRYAG | 4 cut(s) | 1166, 2097, 2232, 2817 |
| BfoI | RGCGCY | 1 cut(s) | 1003 |
| BfuAI | ACCTGC | 3 cut(s) | 89, 2047, 2104 |
| BfuI | GTATCC | 1 cut(s) | 2278 |
| BglI | GCCNNNNNGGC | 1 cut(s) | 39 |
| BglII | AGATCT | 1 cut(s) | 1986 |
| Bme18I | GGWCC | 3 cut(s) | 1400, 2185, 2678 |
| BmgT120I | GGNCC | 9 cut(s) | 40, 58, 59, 143, 144, 1400, 2185, 2661, 2678 |
| BmiI | GGNNCC | 9 cut(s) | 60, 74, 145, 369, 427, 636, 2253, 2464, 2662 |
| BmrI | ACTGGG | 4 cut(s) | 150, 1055, 2081, 2787 |
| BmsI | GCATC | 4 cut(s) | 331, 1522, 1890, 2036 |
| BmtI | GCTAGC | 1 cut(s) | 2181 |
| BmuI | ACTGGG | 4 cut(s) | 150, 1055, 2081, 2787 |
| BpiI | GAAGAC | 4 cut(s) | 752, 1865, 2510, 2849 |
| BpmI | CTGGAG | 1 cut(s) | 1428 |
| Bpu10I | CCTNAGC | 3 cut(s) | 228, 372, 2112 |
| Bpu14I | TTCGAA | 1 cut(s) | 610 |
| BpuEI | CTTGAG | 2 cut(s) | 422, 647 |
| BpuMI | CCSGG | 1 cut(s) | 133 |
| Bsa29I | ATCGAT | 1 cut(s) | 1665 |
| BsaAI | YACGTR | 2 cut(s) | 1445, 1868 |
| BsaBI | GATNNNNATC | 3 cut(s) | 938, 1299, 2604 |
| BsaI | GGTCTC | 5 cut(s) | 475, 570, 2117, 2444, 2474 |
| BsaWI | WCCGGW | 3 cut(s) | 2419, 2528, 2759 |
| BsaXI | ACNNNNNCTCC | 4 cut(s) | 227, 257, 567, 597 |
| Bse118I | RCCGGY | 2 cut(s) | 2528, 2759 |
| Bse1I | ACTGG | 6 cut(s) | 145, 918, 1050, 1182, 2087, 2782 |
| Bse3DI | GCAATG | 5 cut(s) | 314, 866, 1836, 2620, 2760 |
| Bse8I | GATNNNNATC | 3 cut(s) | 938, 1299, 2604 |
| BseBI | CCWGG | 9 cut(s) | 38, 56, 200, 339, 450, 1240, 1407, 1542, 2610 |
| BseCI | ATCGAT | 1 cut(s) | 1665 |
| BseGI | GGATG | 3 cut(s) | 448, 691, 2705 |
| BseJI | GATNNNNATC | 3 cut(s) | 938, 1299, 2604 |
| BseMI | GCAATG | 5 cut(s) | 314, 866, 1836, 2620, 2760 |
| BseMII | CTCAG | 5 cut(s) | 219, 486, 1375, 2126, 2501 |
| BseNI | ACTGG | 6 cut(s) | 145, 918, 1050, 1182, 2087, 2782 |
| BseRI | GAGGAG | 3 cut(s) | 13, 16, 644 |
| BseSI | GKGCMC | 3 cut(s) | 62, 147, 270 |
| BseXI | GCAGC | 9 cut(s) | 306, 395, 820, 1009, 1033, 1180, 1925, 2834, 2873 |
| BseYI | CCCAGC | 3 cut(s) | 1808, 2221, 2657 |
| Bsh1236I | CGCG | 1 cut(s) | 1207 |
| Bsh1285I | CGRYCG | 1 cut(s) | 329 |
| BshFI | GGCC | 7 cut(s) | 42, 60, 145, 159, 239, 1181, 2663 |
| BshNI | GGYRCC | 1 cut(s) | 425 |
| BshTI | ACCGGT | 2 cut(s) | 2528, 2759 |
| BshVI | ATCGAT | 1 cut(s) | 1665 |
| BsiEI | CGRYCG | 1 cut(s) | 329 |
| BsiHKAI | GWGCWC | 2 cut(s) | 96, 1158 |
| BsiSI | CCGG | 5 cut(s) | 132, 2420, 2529, 2760, 2858 |
| BslFI | GGGAC | 3 cut(s) | 466, 749, 1638 |
| BsmFI | GGGAC | 3 cut(s) | 466, 749, 1638 |
| BsmI | GAATGC | 1 cut(s) | 567 |
| BsnI | GGCC | 7 cut(s) | 42, 60, 145, 159, 239, 1181, 2663 |
| Bso31I | GGTCTC | 5 cut(s) | 475, 570, 2117, 2444, 2474 |
| Bsp119I | TTCGAA | 1 cut(s) | 610 |
| Bsp120I | GGGCCC | 2 cut(s) | 58, 143 |
| Bsp1286I | GDGCHC | 6 cut(s) | 62, 75, 96, 147, 270, 1158 |
| Bsp1407I | TGTACA | 1 cut(s) | 1742 |
| Bsp19I | CCATGG | 1 cut(s) | 2454 |
| BspACI | CCGC | 8 cut(s) | 76, 206, 233, 329, 1003, 1993, 2042, 2799 |
| BspANI | GGCC | 7 cut(s) | 42, 60, 145, 159, 239, 1181, 2663 |
| BspCNI | CTCAG | 5 cut(s) | 220, 485, 1374, 2125, 2500 |
| BspDI | ATCGAT | 1 cut(s) | 1665 |
| BspFNI | CGCG | 1 cut(s) | 1207 |
| BspLI | GGNNCC | 9 cut(s) | 60, 74, 145, 369, 427, 636, 2253, 2464, 2662 |
| BspMAI | CTGCAG | 2 cut(s) | 1170, 2101 |
| BspMI | ACCTGC | 3 cut(s) | 89, 2047, 2104 |
| BspOI | GCTAGC | 1 cut(s) | 2181 |
| BspQI | GCTCTTC | 3 cut(s) | 873, 1146, 1923 |
| BspT104I | TTCGAA | 1 cut(s) | 610 |
| BspT107I | GGYRCC | 1 cut(s) | 425 |
| BspTNI | GGTCTC | 5 cut(s) | 475, 570, 2117, 2444, 2474 |
| BsrBI | CCGCTC | 1 cut(s) | 331 |
| BsrDI | GCAATG | 5 cut(s) | 314, 866, 1836, 2620, 2760 |
| BsrFI | RCCGGY | 2 cut(s) | 2528, 2759 |
| BsrGI | TGTACA | 1 cut(s) | 1742 |
| BsrI | ACTGG | 6 cut(s) | 145, 918, 1050, 1182, 2087, 2782 |
| BssAI | RCCGGY | 2 cut(s) | 2528, 2759 |
| BssT1I | CCWWGG | 3 cut(s) | 812, 2280, 2454 |
| Bst2UI | CCWGG | 9 cut(s) | 38, 56, 200, 339, 450, 1240, 1407, 1542, 2610 |
| Bst4CI | ACNGT | 7 cut(s) | 301, 530, 646, 1253, 1457, 2061, 2578 |
| Bst6I | CTCTTC | 5 cut(s) | 873, 972, 1146, 1923, 2286 |
| BstAPI | GCANNNNNTGC | 1 cut(s) | 1079 |
| BstAUI | TGTACA | 1 cut(s) | 1742 |
| BstBAI | YACGTR | 2 cut(s) | 1445, 1868 |
| BstBI | TTCGAA | 1 cut(s) | 610 |
| BstC8I | GCNNGC | 5 cut(s) | 96, 125, 411, 2179, 2889 |
| BstDEI | CTNAG | 6 cut(s) | 228, 372, 472, 1361, 2112, 2487 |
| BstDSI | CCRYGG | 1 cut(s) | 2454 |
| BstENI | CCTNNNNNAGG | 1 cut(s) | 1724 |
| BstF5I | GGATG | 3 cut(s) | 448, 691, 2705 |
| BstFNI | CGCG | 1 cut(s) | 1207 |
| BstH2I | RGCGCY | 1 cut(s) | 1003 |
| BstHHI | GCGC | 2 cut(s) | 1002, 1282 |
| BstMCI | CGRYCG | 1 cut(s) | 329 |
| BstNI | CCWGG | 9 cut(s) | 38, 56, 200, 339, 450, 1240, 1407, 1542, 2610 |
| BstNSI | RCATGY | 4 cut(s) | 352, 1631, 1878, 2651 |
| BstSFI | CTRYAG | 4 cut(s) | 1166, 2097, 2232, 2817 |
| BstSLI | GKGCMC | 3 cut(s) | 62, 147, 270 |
| BstUI | CGCG | 1 cut(s) | 1207 |
| BstV1I | GCAGC | 9 cut(s) | 306, 395, 820, 1009, 1033, 1180, 1925, 2834, 2873 |
| BstV2I | GAAGAC | 4 cut(s) | 752, 1865, 2510, 2849 |
| BstX2I | RGATCY | 6 cut(s) | 367, 634, 1986, 2215, 2605, 2784 |
| BstYI | RGATCY | 6 cut(s) | 367, 634, 1986, 2215, 2605, 2784 |
| Bsu15I | ATCGAT | 1 cut(s) | 1665 |
| BsuI | GTATCC | 1 cut(s) | 2278 |
| BsuRI | GGCC | 7 cut(s) | 42, 60, 145, 159, 239, 1181, 2663 |
| BsuTUI | ATCGAT | 1 cut(s) | 1665 |
| BtgI | CCRYGG | 1 cut(s) | 2454 |
| BtsCI | GGATG | 3 cut(s) | 448, 691, 2705 |
| BtsIMutI | CAGTG | 2 cut(s) | 911, 1258 |
| BveI | ACCTGC | 3 cut(s) | 89, 2047, 2104 |
| Cac8I | GCNNGC | 5 cut(s) | 96, 125, 411, 2179, 2889 |
| CaiI | CAGNNNCTG | 1 cut(s) | 479 |
| CfoI | GCGC | 2 cut(s) | 1002, 1282 |
| Cfr10I | RCCGGY | 2 cut(s) | 2528, 2759 |
| Cfr13I | GGNCC | 9 cut(s) | 40, 58, 59, 143, 144, 1400, 2185, 2661, 2678 |
| ClaI | ATCGAT | 1 cut(s) | 1665 |
| CseI | GACGC | 1 cut(s) | 1213 |
| CsiI | ACCWGGT | 1 cut(s) | 198 |
| Csp6I | GTAC | 4 cut(s) | 546, 1553, 1743, 2559 |
| CspAI | ACCGGT | 2 cut(s) | 2528, 2759 |
| CspCI | CAANNNNNGTGG | 4 cut(s) | 1737, 1772, 2473, 2508 |
| CviQI | GTAC | 4 cut(s) | 546, 1553, 1743, 2559 |
| DdeI | CTNAG | 6 cut(s) | 228, 372, 472, 1361, 2112, 2487 |
| DraI | TTTAAA | 1 cut(s) | 903 |
| EaeI | YGGCCR | 1 cut(s) | 157 |
| Eam1104I | CTCTTC | 5 cut(s) | 873, 972, 1146, 1923, 2286 |
| EarI | CTCTTC | 5 cut(s) | 873, 972, 1146, 1923, 2286 |
| EciI | GGCGGA | 2 cut(s) | 221, 248 |
| Ecl136II | GAGCTC | 2 cut(s) | 94, 1156 |
| Eco130I | CCWWGG | 3 cut(s) | 812, 2280, 2454 |
| Eco24I | GRGCYC | 5 cut(s) | 62, 75, 96, 147, 1158 |
| Eco31I | GGTCTC | 5 cut(s) | 475, 570, 2117, 2444, 2474 |
| Eco47I | GGWCC | 3 cut(s) | 1400, 2185, 2678 |
| Eco53kI | GAGCTC | 2 cut(s) | 94, 1156 |
| Eco57I | CTGAAG | 2 cut(s) | 26, 764 |
| Eco72I | CACGTG | 2 cut(s) | 1445, 1868 |
| EcoICRI | GAGCTC | 2 cut(s) | 94, 1156 |
| EcoNI | CCTNNNNNAGG | 1 cut(s) | 1724 |
| EcoO109I | RGGNCCY | 1 cut(s) | 59 |
| EcoRII | CCWGG | 9 cut(s) | 36, 54, 198, 337, 448, 1238, 1405, 1540, 2608 |
| EcoT14I | CCWWGG | 3 cut(s) | 812, 2280, 2454 |
| EcoT38I | GRGCYC | 5 cut(s) | 62, 75, 96, 147, 1158 |
| ErhI | CCWWGG | 3 cut(s) | 812, 2280, 2454 |
| FalI | AAGNNNNNCTT | 4 cut(s) | 2502, 2534, 2895, 2927 |
| FaqI | GGGAC | 3 cut(s) | 466, 749, 1638 |
| FauI | CCCGC | 1 cut(s) | 2792 |
| FbaI | TGATCA | 1 cut(s) | 2410 |
| FokI | GGATG | 3 cut(s) | 455, 698, 2692 |
| FriOI | GRGCYC | 5 cut(s) | 62, 75, 96, 147, 1158 |
| FspBI | CTAG | 9 cut(s) | 462, 750, 884, 920, 1217, 1842, 2070, 2178, 2682 |
| GlaI | GCGC | 2 cut(s) | 1001, 1281 |
| GsaI | CCCAGC | 3 cut(s) | 1812, 2225, 2661 |
| GsuI | CTGGAG | 1 cut(s) | 1428 |
| HaeII | RGCGCY | 1 cut(s) | 1003 |
| HaeIII | GGCC | 7 cut(s) | 42, 60, 145, 159, 239, 1181, 2663 |
| HapII | CCGG | 5 cut(s) | 132, 2420, 2529, 2760, 2858 |
| HgaI | GACGC | 1 cut(s) | 1213 |
| HhaI | GCGC | 2 cut(s) | 1002, 1282 |
| Hin6I | GCGC | 2 cut(s) | 1000, 1280 |
| HinP1I | GCGC | 2 cut(s) | 1000, 1280 |
| HincII | GTYRAC | 5 cut(s) | 138, 655, 1227, 2350, 2534 |
| HindII | GTYRAC | 5 cut(s) | 138, 655, 1227, 2350, 2534 |
| HindIII | AAGCTT | 2 cut(s) | 8, 2636 |
| HpaII | CCGG | 5 cut(s) | 132, 2420, 2529, 2760, 2858 |
| HphI | GGTGA | 7 cut(s) | 121, 809, 1004, 1646, 2252, 2774, 2975 |
| Hpy166II | GTNNAC | 8 cut(s) | 49, 138, 655, 1227, 1403, 2350, 2534, 2920 |
| Hpy8I | GTNNAC | 8 cut(s) | 49, 138, 655, 1227, 1403, 2350, 2534, 2920 |
| Hpy99I | CGWCG | 1 cut(s) | 1521 |
| HpyCH4III | ACNGT | 7 cut(s) | 301, 530, 646, 1253, 1457, 2061, 2578 |
| HpyCH4IV | ACGT | 9 cut(s) | 582, 707, 738, 898, 1444, 1707, 1867, 2169, 2916 |
| HpyF3I | CTNAG | 6 cut(s) | 228, 372, 472, 1361, 2112, 2487 |
| HpySE526I | ACGT | 9 cut(s) | 582, 707, 738, 898, 1444, 1707, 1867, 2169, 2916 |
| HspAI | GCGC | 2 cut(s) | 1000, 1280 |
| Ksp22I | TGATCA | 1 cut(s) | 2410 |
| LguI | GCTCTTC | 3 cut(s) | 873, 1146, 1923 |
| LmnI | GCTCC | 5 cut(s) | 78, 418, 830, 1657, 2024 |
| Lsp1109I | GCAGC | 9 cut(s) | 306, 395, 820, 1009, 1033, 1180, 1925, 2834, 2873 |
| LweI | GCATC | 4 cut(s) | 331, 1522, 1890, 2036 |
| MabI | ACCWGGT | 1 cut(s) | 198 |
| MaeI | CTAG | 9 cut(s) | 462, 750, 884, 920, 1217, 1842, 2070, 2178, 2682 |
| MaeII | ACGT | 9 cut(s) | 582, 707, 738, 898, 1444, 1707, 1867, 2169, 2916 |
| MaeIII | GTNAC | 5 cut(s) | 1201, 1371, 1903, 2524, 2767 |
| MbiI | CCGCTC | 1 cut(s) | 331 |
| MfeI | CAATTG | 4 cut(s) | 261, 972, 1437, 1713 |
| MflI | RGATCY | 6 cut(s) | 367, 634, 1986, 2215, 2605, 2784 |
| MhlI | GDGCHC | 6 cut(s) | 62, 75, 96, 147, 270, 1158 |
| MluI | ACGCGT | 1 cut(s) | 1205 |
| MlyI | GAGTC | 3 cut(s) | 54, 251, 2410 |
| MmeI | TCCRAC | 3 cut(s) | 1155, 1635, 2404 |
| MroXI | GAANNNNTTC | 1 cut(s) | 2148 |
| MslI | CAYNNNNRTG | 4 cut(s) | 795, 1632, 2646, 2723 |
| MspA1I | CMGCKG | 1 cut(s) | 1171 |
| MspI | CCGG | 5 cut(s) | 132, 2420, 2529, 2760, 2858 |
| MunI | CAATTG | 4 cut(s) | 261, 972, 1437, 1713 |
| Mva1269I | GAATGC | 1 cut(s) | 567 |
| MvaI | CCWGG | 9 cut(s) | 38, 56, 200, 339, 450, 1240, 1407, 1542, 2610 |
| MvnI | CGCG | 1 cut(s) | 1207 |
| NciI | CCSGG | 1 cut(s) | 133 |
| NcoI | CCATGG | 1 cut(s) | 2454 |
| NheI | GCTAGC | 1 cut(s) | 2177 |
| NlaIV | GGNNCC | 9 cut(s) | 60, 74, 145, 369, 427, 636, 2253, 2464, 2662 |
| NmeAIII | GCCGAG | 4 cut(s) | 68, 185, 265, 1970 |
| NmuCI | GTSAC | 3 cut(s) | 1201, 1371, 1903 |
| NspI | RCATGY | 4 cut(s) | 352, 1631, 1878, 2651 |
| NspV | TTCGAA | 1 cut(s) | 610 |
| PaqCI | CACCTGC | 1 cut(s) | 89 |
| PasI | CCCWGGG | 2 cut(s) | 37, 1239 |
| PciI | ACATGT | 1 cut(s) | 2647 |
| PciSI | GCTCTTC | 3 cut(s) | 873, 1146, 1923 |
| PcsI | WCGNNNNNNNCGW | 2 cut(s) | 305, 2124 |
| PctI | GAATGC | 1 cut(s) | 567 |
| PdmI | GAANNNNTTC | 1 cut(s) | 2148 |
| PfeI | GAWTC | 9 cut(s) | 274, 949, 956, 1288, 1470, 1963, 2201, 2276, 2630 |
| PflMI | CCANNNNNTGG | 3 cut(s) | 55, 1239, 2675 |
| PinAI | ACCGGT | 2 cut(s) | 2528, 2759 |
| PleI | GAGTC | 3 cut(s) | 53, 250, 2410 |
| PmaCI | CACGTG | 2 cut(s) | 1445, 1868 |
| PmlI | CACGTG | 2 cut(s) | 1445, 1868 |
| PpsI | GAGTC | 3 cut(s) | 53, 250, 2410 |
| Ppu21I | YACGTR | 2 cut(s) | 1445, 1868 |
| PscI | ACATGT | 1 cut(s) | 2647 |
| PsiI | TTATAA | 2 cut(s) | 678, 894 |
| Psp124BI | GAGCTC | 2 cut(s) | 96, 1158 |
| Psp1406I | AACGTT | 1 cut(s) | 898 |
| Psp6I | CCWGG | 9 cut(s) | 36, 54, 198, 337, 448, 1238, 1405, 1540, 2608 |
| PspCI | CACGTG | 2 cut(s) | 1445, 1868 |
| PspFI | CCCAGC | 3 cut(s) | 1808, 2221, 2657 |
| PspGI | CCWGG | 9 cut(s) | 36, 54, 198, 337, 448, 1238, 1405, 1540, 2608 |
| PspN4I | GGNNCC | 9 cut(s) | 60, 74, 145, 369, 427, 636, 2253, 2464, 2662 |
| PspOMI | GGGCCC | 2 cut(s) | 58, 143 |
| PspPI | GGNCC | 9 cut(s) | 40, 58, 59, 143, 144, 1400, 2185, 2661, 2678 |
| PstI | CTGCAG | 2 cut(s) | 1170, 2101 |
| PstNI | CAGNNNCTG | 1 cut(s) | 479 |
| PsuI | RGATCY | 6 cut(s) | 367, 634, 1986, 2215, 2605, 2784 |
| PvuII | CAGCTG | 1 cut(s) | 1171 |
| RsaI | GTAC | 4 cut(s) | 547, 1554, 1744, 2560 |
| RsaNI | GTAC | 4 cut(s) | 546, 1553, 1743, 2559 |
| RseI | CAYNNNNRTG | 4 cut(s) | 795, 1632, 2646, 2723 |
| SacI | GAGCTC | 2 cut(s) | 96, 1158 |
| SapI | GCTCTTC | 3 cut(s) | 873, 1146, 1923 |
| Sau96I | GGNCC | 9 cut(s) | 40, 58, 59, 143, 144, 1400, 2185, 2661, 2678 |
| SchI | GAGTC | 3 cut(s) | 54, 251, 2410 |
| SduI | GDGCHC | 6 cut(s) | 62, 75, 96, 147, 270, 1158 |
| SexAI | ACCWGGT | 1 cut(s) | 198 |
| SfaNI | GCATC | 4 cut(s) | 331, 1522, 1890, 2036 |
| SfcI | CTRYAG | 4 cut(s) | 1166, 2097, 2232, 2817 |
| SfuI | TTCGAA | 1 cut(s) | 610 |
| SinI | GGWCC | 3 cut(s) | 1400, 2185, 2678 |
| SmiMI | CAYNNNNRTG | 4 cut(s) | 795, 1632, 2646, 2723 |
| SmlI | CTYRAG | 2 cut(s) | 437, 662 |
| SmoI | CTYRAG | 2 cut(s) | 437, 662 |
| SpeI | ACTAGT | 3 cut(s) | 749, 919, 2069 |
| SsiI | CCGC | 8 cut(s) | 76, 206, 233, 329, 1003, 1993, 2042, 2799 |
| SspMI | CTAG | 9 cut(s) | 462, 750, 884, 920, 1217, 1842, 2070, 2178, 2682 |
| SstI | GAGCTC | 2 cut(s) | 96, 1158 |
| StyI | CCWWGG | 3 cut(s) | 812, 2280, 2454 |
| TaaI | ACNGT | 7 cut(s) | 301, 530, 646, 1253, 1457, 2061, 2578 |
| TaiI | ACGT | 9 cut(s) | 585, 710, 741, 901, 1447, 1710, 1870, 2172, 2919 |
| TaqII | GACCGA | 1 cut(s) | 2141 |
| TatI | WGTACW | 1 cut(s) | 1742 |
| TauI | GCSGC | 1 cut(s) | 1005 |
| TfiI | GAWTC | 9 cut(s) | 274, 949, 956, 1288, 1470, 1963, 2201, 2276, 2630 |
| TscAI | CASTG | 2 cut(s) | 918, 1258 |
| TseFI | GTSAC | 3 cut(s) | 1201, 1371, 1903 |
| TseI | GCWGC | 9 cut(s) | 319, 383, 833, 997, 1021, 1168, 1913, 2822, 2861 |
| Tsp45I | GTSAC | 3 cut(s) | 1201, 1371, 1903 |
| TspRI | CASTG | 2 cut(s) | 918, 1258 |
| Van91I | CCANNNNNTGG | 3 cut(s) | 55, 1239, 2675 |
| VpaK11BI | GGWCC | 3 cut(s) | 1400, 2185, 2678 |
| XagI | CCTNNNNNAGG | 1 cut(s) | 1724 |
| XapI | RAATTY | 3 cut(s) | 1193, 1340, 2304 |
| XceI | RCATGY | 4 cut(s) | 352, 1631, 1878, 2651 |
| XcmI | CCANNNNNNNNNTGG | 1 cut(s) | 1777 |
| XmnI | GAANNNNTTC | 1 cut(s) | 2148 |
| XspI | CTAG | 9 cut(s) | 462, 750, 884, 920, 1217, 1842, 2070, 2178, 2682 |