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 | 1 cut(s) | 900 |
| AarI | CACCTGC | 2 cut(s) | 1949, 2654 |
| Acc36I | ACCTGC | 3 cut(s) | 1949, 2245, 2654 |
| AccB1I | GGYRCC | 1 cut(s) | 2666 |
| AccB7I | CCANNNNNTGG | 2 cut(s) | 1245, 2681 |
| AccII | CGCG | 2 cut(s) | 182, 1213 |
| AccIII | TCCGGA | 1 cut(s) | 1675 |
| AciI | CCGC | 6 cut(s) | 227, 326, 1009, 1999, 2805, 2828 |
| AclI | AACGTT | 1 cut(s) | 904 |
| AcoI | YGGCCR | 1 cut(s) | 1435 |
| AcsI | RAATTY | 2 cut(s) | 1199, 2310 |
| AcuI | CTGAAG | 3 cut(s) | 26, 770, 2067 |
| AcvI | CACGTG | 1 cut(s) | 1874 |
| AfaI | GTAC | 5 cut(s) | 553, 1560, 1750, 2566, 2701 |
| AflIII | ACRYGT | 2 cut(s) | 1211, 1871 |
| AhlI | ACTAGT | 2 cut(s) | 755, 925 |
| AjnI | CCWGG | 6 cut(s) | 36, 54, 343, 1244, 1411, 1546 |
| AjuI | GAANNNNNNNTTGG | 2 cut(s) | 2226, 2258 |
| Alw21I | GWGCWC | 2 cut(s) | 51, 96 |
| Alw44I | GTGCAC | 1 cut(s) | 47 |
| AlwNI | CAGNNNCTG | 3 cut(s) | 485, 2132, 2267 |
| Ama87I | CYCGRG | 2 cut(s) | 42, 80 |
| Aor13HI | TCCGGA | 1 cut(s) | 1675 |
| ApaI | GGGCCC | 1 cut(s) | 87 |
| ApaLI | GTGCAC | 1 cut(s) | 47 |
| ApeKI | GCWGC | 6 cut(s) | 389, 839, 1027, 1174, 1919, 2867 |
| ApoI | RAATTY | 2 cut(s) | 1199, 2310 |
| AspLEI | GCGC | 1 cut(s) | 1008 |
| AsuC2I | CCSGG | 4 cut(s) | 81, 82, 133, 456 |
| AsuHPI | GGTGA | 7 cut(s) | 121, 815, 1010, 1652, 2048, 2258, 2852 |
| AsuII | TTCGAA | 1 cut(s) | 616 |
| AvaI | CYCGRG | 2 cut(s) | 42, 80 |
| AvaII | GGWCC | 4 cut(s) | 59, 1527, 2684, 2850 |
| BaeGI | GKGCMC | 3 cut(s) | 51, 87, 276 |
| BamHI | GGATCC | 3 cut(s) | 373, 640, 2790 |
| BanI | GGYRCC | 1 cut(s) | 2666 |
| BanII | GRGCYC | 3 cut(s) | 87, 96, 1288 |
| BbrPI | CACGTG | 1 cut(s) | 1874 |
| BbsI | GAAGAC | 3 cut(s) | 249, 758, 1871 |
| Bbv12I | GWGCWC | 2 cut(s) | 51, 96 |
| BbvI | GCAGC | 6 cut(s) | 401, 826, 1039, 1186, 1931, 2879 |
| BccI | CCATC | 5 cut(s) | 622, 1549, 2081, 2675, 2861 |
| BceAI | ACGGC | 6 cut(s) | 158, 304, 428, 1340, 1422, 2090 |
| BciT130I | CCWGG | 6 cut(s) | 38, 56, 345, 1246, 1413, 1548 |
| BclI | TGATCA | 3 cut(s) | 196, 661, 2706 |
| BcnI | CCSGG | 4 cut(s) | 81, 82, 133, 456 |
| BcuI | ACTAGT | 2 cut(s) | 755, 925 |
| BfaI | CTAG | 8 cut(s) | 468, 756, 890, 926, 1848, 2165, 2184, 2688 |
| BfmI | CTRYAG | 5 cut(s) | 1172, 1482, 2238, 2661, 2865 |
| BfoI | RGCGCY | 1 cut(s) | 1009 |
| BfuAI | ACCTGC | 3 cut(s) | 1949, 2245, 2654 |
| BglII | AGATCT | 1 cut(s) | 1992 |
| BisI | GCNGC | 9 cut(s) | 326, 390, 840, 1009, 1028, 1175, 1920, 2829, 2868 |
| BlsI | GCNGC | 9 cut(s) | 327, 391, 841, 1010, 1029, 1176, 1921, 2830, 2869 |
| Bme18I | GGWCC | 4 cut(s) | 59, 1527, 2684, 2850 |
| BmeT110I | CYCGRG | 2 cut(s) | 42, 80 |
| BmiI | GGNNCC | 9 cut(s) | 60, 61, 85, 375, 642, 1970, 2470, 2668, 2792 |
| BmrI | ACTGGG | 3 cut(s) | 1061, 2222, 2793 |
| BmsI | GCATC | 3 cut(s) | 1528, 1896, 2281 |
| BmuI | ACTGGG | 3 cut(s) | 1061, 2222, 2793 |
| BpiI | GAAGAC | 3 cut(s) | 249, 758, 1871 |
| BplI | GAGNNNNNCTC | 4 cut(s) | 83, 115, 1790, 1822 |
| BpmI | CTGGAG | 3 cut(s) | 20, 1434, 2409 |
| Bpu10I | CCTNAGC | 1 cut(s) | 2118 |
| Bpu14I | TTCGAA | 1 cut(s) | 616 |
| BpuEI | CTTGAG | 2 cut(s) | 428, 653 |
| BpuMI | CCSGG | 4 cut(s) | 81, 82, 133, 456 |
| Bsa29I | ATCGAT | 1 cut(s) | 1605 |
| BsaAI | YACGTR | 1 cut(s) | 1874 |
| BsaBI | GATNNNNATC | 3 cut(s) | 639, 944, 1305 |
| BsaI | GGTCTC | 4 cut(s) | 481, 576, 2450, 2480 |
| BsaJI | CCNNGG | 9 cut(s) | 55, 80, 455, 818, 1244, 1245, 2142, 2286, 2460 |
| BsaWI | WCCGGW | 1 cut(s) | 1675 |
| BsaXI | ACNNNNNCTCC | 2 cut(s) | 573, 603 |
| Bse118I | RCCGGY | 1 cut(s) | 428 |
| Bse1I | ACTGG | 7 cut(s) | 924, 1056, 1188, 2228, 2426, 2539, 2788 |
| Bse3DI | GCAATG | 4 cut(s) | 872, 1809, 1842, 2766 |
| Bse8I | GATNNNNATC | 3 cut(s) | 639, 944, 1305 |
| BseAI | TCCGGA | 1 cut(s) | 1675 |
| BseBI | CCWGG | 6 cut(s) | 38, 56, 345, 1246, 1413, 1548 |
| BseCI | ATCGAT | 1 cut(s) | 1605 |
| BseDI | CCNNGG | 9 cut(s) | 55, 80, 455, 818, 1244, 1245, 2142, 2286, 2460 |
| BseGI | GGATG | 6 cut(s) | 454, 697, 2296, 2554, 2686, 2711 |
| BseJI | GATNNNNATC | 3 cut(s) | 639, 944, 1305 |
| BseMI | GCAATG | 4 cut(s) | 872, 1809, 1842, 2766 |
| BseMII | CTCAG | 4 cut(s) | 492, 806, 2132, 2507 |
| BseNI | ACTGG | 7 cut(s) | 924, 1056, 1188, 2228, 2426, 2539, 2788 |
| BseSI | GKGCMC | 3 cut(s) | 51, 87, 276 |
| BseXI | GCAGC | 6 cut(s) | 401, 826, 1039, 1186, 1931, 2879 |
| BseYI | CCCAGC | 1 cut(s) | 1814 |
| Bsh1236I | CGCG | 2 cut(s) | 182, 1213 |
| BshNI | GGYRCC | 1 cut(s) | 2666 |
| BshVI | ATCGAT | 1 cut(s) | 1605 |
| BsiHKAI | GWGCWC | 2 cut(s) | 51, 96 |
| BsiHKCI | CYCGRG | 2 cut(s) | 42, 80 |
| BsiSI | CCGG | 5 cut(s) | 81, 132, 429, 455, 1676 |
| BslFI | GGGAC | 5 cut(s) | 45, 63, 472, 1644, 2707 |
| BsmBI | CGTCTC | 2 cut(s) | 159, 2210 |
| BsmFI | GGGAC | 5 cut(s) | 45, 63, 472, 1644, 2707 |
| BsmI | GAATGC | 1 cut(s) | 573 |
| Bso31I | GGTCTC | 4 cut(s) | 481, 576, 2450, 2480 |
| BsoBI | CYCGRG | 2 cut(s) | 42, 80 |
| Bsp119I | TTCGAA | 1 cut(s) | 616 |
| Bsp120I | GGGCCC | 1 cut(s) | 83 |
| Bsp1286I | GDGCHC | 5 cut(s) | 51, 87, 96, 276, 1288 |
| Bsp13I | TCCGGA | 1 cut(s) | 1675 |
| Bsp1407I | TGTACA | 1 cut(s) | 1748 |
| Bsp19I | CCATGG | 1 cut(s) | 2460 |
| BspACI | CCGC | 6 cut(s) | 227, 326, 1009, 1999, 2805, 2828 |
| BspCNI | CTCAG | 4 cut(s) | 491, 805, 2131, 2506 |
| BspDI | ATCGAT | 1 cut(s) | 1605 |
| BspEI | TCCGGA | 1 cut(s) | 1675 |
| BspFNI | CGCG | 2 cut(s) | 182, 1213 |
| BspLI | GGNNCC | 9 cut(s) | 60, 61, 85, 375, 642, 1970, 2470, 2668, 2792 |
| BspMAI | CTGCAG | 4 cut(s) | 1176, 2242, 2665, 2869 |
| BspMI | ACCTGC | 3 cut(s) | 1949, 2245, 2654 |
| BspQI | GCTCTTC | 2 cut(s) | 879, 1929 |
| BspT104I | TTCGAA | 1 cut(s) | 616 |
| BspT107I | GGYRCC | 1 cut(s) | 2666 |
| BspTNI | GGTCTC | 4 cut(s) | 481, 576, 2450, 2480 |
| BsrDI | GCAATG | 4 cut(s) | 872, 1809, 1842, 2766 |
| BsrFI | RCCGGY | 1 cut(s) | 428 |
| BsrGI | TGTACA | 1 cut(s) | 1748 |
| BsrI | ACTGG | 7 cut(s) | 924, 1056, 1188, 2228, 2426, 2539, 2788 |
| BssAI | RCCGGY | 1 cut(s) | 428 |
| BssECI | CCNNGG | 9 cut(s) | 55, 80, 455, 818, 1244, 1245, 2142, 2286, 2460 |
| BssT1I | CCWWGG | 4 cut(s) | 818, 2142, 2286, 2460 |
| Bst2UI | CCWGG | 6 cut(s) | 38, 56, 345, 1246, 1413, 1548 |
| Bst4CI | ACNGT | 6 cut(s) | 307, 652, 1259, 1463, 2338, 2584 |
| Bst6I | CTCTTC | 4 cut(s) | 22, 879, 978, 1929 |
| BstAUI | TGTACA | 1 cut(s) | 1748 |
| BstBAI | YACGTR | 1 cut(s) | 1874 |
| BstBI | TTCGAA | 1 cut(s) | 616 |
| BstC8I | GCNNGC | 7 cut(s) | 96, 125, 184, 417, 539, 558, 872 |
| BstDEI | CTNAG | 8 cut(s) | 252, 478, 792, 1222, 1367, 1594, 2118, 2493 |
| BstDSI | CCRYGG | 1 cut(s) | 2460 |
| BstENI | CCTNNNNNAGG | 1 cut(s) | 1730 |
| BstF5I | GGATG | 6 cut(s) | 454, 697, 2296, 2554, 2686, 2711 |
| BstFNI | CGCG | 2 cut(s) | 182, 1213 |
| BstH2I | RGCGCY | 1 cut(s) | 1009 |
| BstHHI | GCGC | 1 cut(s) | 1008 |
| BstNI | CCWGG | 6 cut(s) | 38, 56, 345, 1246, 1413, 1548 |
| BstNSI | RCATGY | 3 cut(s) | 358, 1637, 1884 |
| BstSFI | CTRYAG | 5 cut(s) | 1172, 1482, 2238, 2661, 2865 |
| BstSLI | GKGCMC | 3 cut(s) | 51, 87, 276 |
| BstUI | CGCG | 2 cut(s) | 182, 1213 |
| BstV1I | GCAGC | 6 cut(s) | 401, 826, 1039, 1186, 1931, 2879 |
| BstV2I | GAAGAC | 3 cut(s) | 249, 758, 1871 |
| BstX2I | RGATCY | 5 cut(s) | 373, 640, 1992, 2221, 2790 |
| BstYI | RGATCY | 5 cut(s) | 373, 640, 1992, 2221, 2790 |
| Bsu15I | ATCGAT | 1 cut(s) | 1605 |
| BsuTUI | ATCGAT | 1 cut(s) | 1605 |
| BtgI | CCRYGG | 1 cut(s) | 2460 |
| BtsCI | GGATG | 6 cut(s) | 454, 697, 2296, 2554, 2686, 2711 |
| BtsIMutI | CAGTG | 4 cut(s) | 917, 1264, 2580, 2974 |
| BveI | ACCTGC | 3 cut(s) | 1949, 2245, 2654 |
| Cac8I | GCNNGC | 7 cut(s) | 96, 125, 184, 417, 539, 558, 872 |
| CaiI | CAGNNNCTG | 3 cut(s) | 485, 2132, 2267 |
| CfoI | GCGC | 1 cut(s) | 1008 |
| Cfr10I | RCCGGY | 1 cut(s) | 428 |
| Cfr9I | CCCGGG | 1 cut(s) | 80 |
| ClaI | ATCGAT | 1 cut(s) | 1605 |
| CseI | GACGC | 2 cut(s) | 188, 1219 |
| Csp6I | GTAC | 5 cut(s) | 552, 1559, 1749, 2565, 2700 |
| CspCI | CAANNNNNGTGG | 4 cut(s) | 1743, 1778, 2479, 2514 |
| CviQI | GTAC | 5 cut(s) | 552, 1559, 1749, 2565, 2700 |
| DdeI | CTNAG | 8 cut(s) | 252, 478, 792, 1222, 1367, 1594, 2118, 2493 |
| DraI | TTTAAA | 1 cut(s) | 909 |
| EaeI | YGGCCR | 1 cut(s) | 1435 |
| Eam1104I | CTCTTC | 4 cut(s) | 22, 879, 978, 1929 |
| EarI | CTCTTC | 4 cut(s) | 22, 879, 978, 1929 |
| Ecl136II | GAGCTC | 1 cut(s) | 94 |
| Eco130I | CCWWGG | 4 cut(s) | 818, 2142, 2286, 2460 |
| Eco24I | GRGCYC | 3 cut(s) | 87, 96, 1288 |
| Eco31I | GGTCTC | 4 cut(s) | 481, 576, 2450, 2480 |
| Eco47I | GGWCC | 4 cut(s) | 59, 1527, 2684, 2850 |
| Eco53kI | GAGCTC | 1 cut(s) | 94 |
| Eco57I | CTGAAG | 3 cut(s) | 26, 770, 2067 |
| Eco72I | CACGTG | 1 cut(s) | 1874 |
| Eco88I | CYCGRG | 2 cut(s) | 42, 80 |
| EcoICRI | GAGCTC | 1 cut(s) | 94 |
| EcoNI | CCTNNNNNAGG | 1 cut(s) | 1730 |
| EcoO109I | RGGNCCY | 1 cut(s) | 59 |
| EcoRII | CCWGG | 6 cut(s) | 36, 54, 343, 1244, 1411, 1546 |
| EcoT14I | CCWWGG | 4 cut(s) | 818, 2142, 2286, 2460 |
| EcoT38I | GRGCYC | 3 cut(s) | 87, 96, 1288 |
| ErhI | CCWWGG | 4 cut(s) | 818, 2142, 2286, 2460 |
| Esp3I | CGTCTC | 2 cut(s) | 159, 2210 |
| FalI | AAGNNNNNCTT | 6 cut(s) | 579, 611, 2508, 2540, 2901, 2933 |
| FaqI | GGGAC | 5 cut(s) | 45, 63, 472, 1644, 2707 |
| FauI | CCCGC | 2 cut(s) | 220, 2798 |
| FauNDI | CATATG | 1 cut(s) | 424 |
| FbaI | TGATCA | 3 cut(s) | 196, 661, 2706 |
| Fnu4HI | GCNGC | 9 cut(s) | 326, 390, 840, 1009, 1028, 1175, 1920, 2829, 2868 |
| FokI | GGATG | 6 cut(s) | 461, 704, 2303, 2561, 2693, 2698 |
| FriOI | GRGCYC | 3 cut(s) | 87, 96, 1288 |
| Fsp4HI | GCNGC | 9 cut(s) | 326, 390, 840, 1009, 1028, 1175, 1920, 2829, 2868 |
| FspBI | CTAG | 8 cut(s) | 468, 756, 890, 926, 1848, 2165, 2184, 2688 |
| GlaI | GCGC | 1 cut(s) | 1007 |
| GluI | GCNGC | 9 cut(s) | 326, 390, 840, 1009, 1028, 1175, 1920, 2829, 2868 |
| GsaI | CCCAGC | 1 cut(s) | 1818 |
| GsuI | CTGGAG | 3 cut(s) | 20, 1434, 2409 |
| HaeII | RGCGCY | 1 cut(s) | 1009 |
| HapII | CCGG | 5 cut(s) | 81, 132, 429, 455, 1676 |
| HgaI | GACGC | 2 cut(s) | 188, 1219 |
| HhaI | GCGC | 1 cut(s) | 1008 |
| Hin6I | GCGC | 1 cut(s) | 1006 |
| HinP1I | GCGC | 1 cut(s) | 1006 |
| HincII | GTYRAC | 4 cut(s) | 138, 1233, 2341, 2540 |
| HindII | GTYRAC | 4 cut(s) | 138, 1233, 2341, 2540 |
| HindIII | AAGCTT | 2 cut(s) | 8, 2642 |
| HpaII | CCGG | 5 cut(s) | 81, 132, 429, 455, 1676 |
| HphI | GGTGA | 7 cut(s) | 121, 815, 1010, 1652, 2048, 2258, 2852 |
| Hpy166II | GTNNAC | 7 cut(s) | 49, 138, 1001, 1233, 2341, 2540, 2926 |
| Hpy188III | TCNNGA | 9 cut(s) | 959, 1298, 1360, 1670, 1676, 1709, 2315, 2746, 2918 |
| Hpy8I | GTNNAC | 7 cut(s) | 49, 138, 1001, 1233, 2341, 2540, 2926 |
| Hpy99I | CGWCG | 4 cut(s) | 162, 191, 1361, 1527 |
| HpyAV | CCTTC | 8 cut(s) | 364, 1039, 1620, 2498, 2743, 2804, 2872, 2906 |
| HpyCH4III | ACNGT | 6 cut(s) | 307, 652, 1259, 1463, 2338, 2584 |
| HpyCH4IV | ACGT | 3 cut(s) | 904, 1873, 2367 |
| HpyF3I | CTNAG | 8 cut(s) | 252, 478, 792, 1222, 1367, 1594, 2118, 2493 |
| HpySE526I | ACGT | 3 cut(s) | 904, 1873, 2367 |
| HspAI | GCGC | 1 cut(s) | 1006 |
| KflI | GGGWCCC | 1 cut(s) | 59 |
| Kpn2I | TCCGGA | 1 cut(s) | 1675 |
| Ksp22I | TGATCA | 3 cut(s) | 196, 661, 2706 |
| LguI | GCTCTTC | 2 cut(s) | 879, 1929 |
| LmnI | GCTCC | 4 cut(s) | 424, 836, 1663, 1678 |
| Lsp1109I | GCAGC | 6 cut(s) | 401, 826, 1039, 1186, 1931, 2879 |
| LweI | GCATC | 3 cut(s) | 1528, 1896, 2281 |
| MaeI | CTAG | 8 cut(s) | 468, 756, 890, 926, 1848, 2165, 2184, 2688 |
| MaeII | ACGT | 3 cut(s) | 904, 1873, 2367 |
| MaeIII | GTNAC | 4 cut(s) | 1207, 1909, 2530, 2773 |
| MfeI | CAATTG | 4 cut(s) | 267, 978, 1443, 1719 |
| MflI | RGATCY | 5 cut(s) | 373, 640, 1992, 2221, 2790 |
| MhlI | GDGCHC | 5 cut(s) | 51, 87, 96, 276, 1288 |
| MluI | ACGCGT | 1 cut(s) | 1211 |
| MlyI | GAGTC | 3 cut(s) | 257, 2075, 2416 |
| MmeI | TCCRAC | 4 cut(s) | 1161, 1505, 1641, 2410 |
| MroI | TCCGGA | 1 cut(s) | 1675 |
| MslI | CAYNNNNRTG | 4 cut(s) | 801, 1638, 2652, 2714 |
| MspA1I | CMGCKG | 1 cut(s) | 1177 |
| MspI | CCGG | 5 cut(s) | 81, 132, 429, 455, 1676 |
| MunI | CAATTG | 4 cut(s) | 267, 978, 1443, 1719 |
| Mva1269I | GAATGC | 1 cut(s) | 573 |
| MvaI | CCWGG | 6 cut(s) | 38, 56, 345, 1246, 1413, 1548 |
| MvnI | CGCG | 2 cut(s) | 182, 1213 |
| NciI | CCSGG | 4 cut(s) | 81, 82, 133, 456 |
| NcoI | CCATGG | 1 cut(s) | 2460 |
| NdeI | CATATG | 1 cut(s) | 424 |
| NlaIV | GGNNCC | 9 cut(s) | 60, 61, 85, 375, 642, 1970, 2470, 2668, 2792 |
| NmeAIII | GCCGAG | 2 cut(s) | 271, 1976 |
| NmuCI | GTSAC | 2 cut(s) | 1207, 1909 |
| NspI | RCATGY | 3 cut(s) | 358, 1637, 1884 |
| NspV | TTCGAA | 1 cut(s) | 616 |
| PaqCI | CACCTGC | 2 cut(s) | 1949, 2654 |
| PasI | CCCWGGG | 1 cut(s) | 1245 |
| PciSI | GCTCTTC | 2 cut(s) | 879, 1929 |
| PctI | GAATGC | 1 cut(s) | 573 |
| PflFI | GACNNNGTC | 1 cut(s) | 2345 |
| PflMI | CCANNNNNTGG | 2 cut(s) | 1245, 2681 |
| PfoI | TCCNGGA | 1 cut(s) | 343 |
| PkrI | GCNGC | 9 cut(s) | 327, 391, 841, 1010, 1029, 1176, 1921, 2830, 2869 |
| PleI | GAGTC | 3 cut(s) | 256, 2074, 2416 |
| PmaCI | CACGTG | 1 cut(s) | 1874 |
| PmlI | CACGTG | 1 cut(s) | 1874 |
| PpsI | GAGTC | 3 cut(s) | 256, 2074, 2416 |
| Ppu21I | YACGTR | 1 cut(s) | 1874 |
| PpuMI | RGGWCCY | 1 cut(s) | 59 |
| PsiI | TTATAA | 1 cut(s) | 900 |
| Psp124BI | GAGCTC | 1 cut(s) | 96 |
| Psp1406I | AACGTT | 1 cut(s) | 904 |
| Psp5II | RGGWCCY | 1 cut(s) | 59 |
| Psp6I | CCWGG | 6 cut(s) | 36, 54, 343, 1244, 1411, 1546 |
| PspCI | CACGTG | 1 cut(s) | 1874 |
| PspFI | CCCAGC | 1 cut(s) | 1814 |
| PspGI | CCWGG | 6 cut(s) | 36, 54, 343, 1244, 1411, 1546 |
| PspN4I | GGNNCC | 9 cut(s) | 60, 61, 85, 375, 642, 1970, 2470, 2668, 2792 |
| PspOMI | GGGCCC | 1 cut(s) | 83 |
| PspPPI | RGGWCCY | 1 cut(s) | 59 |
| PstI | CTGCAG | 4 cut(s) | 1176, 2242, 2665, 2869 |
| PstNI | CAGNNNCTG | 3 cut(s) | 485, 2132, 2267 |
| PsuI | RGATCY | 5 cut(s) | 373, 640, 1992, 2221, 2790 |
| PsyI | GACNNNGTC | 1 cut(s) | 2345 |
| PvuII | CAGCTG | 1 cut(s) | 1177 |
| RsaI | GTAC | 5 cut(s) | 553, 1560, 1750, 2566, 2701 |
| RsaNI | GTAC | 5 cut(s) | 552, 1559, 1749, 2565, 2700 |
| RseI | CAYNNNNRTG | 4 cut(s) | 801, 1638, 2652, 2714 |
| SacI | GAGCTC | 1 cut(s) | 96 |
| SapI | GCTCTTC | 2 cut(s) | 879, 1929 |
| SatI | GCNGC | 9 cut(s) | 326, 390, 840, 1009, 1028, 1175, 1920, 2829, 2868 |
| SbfI | CCTGCAGG | 1 cut(s) | 2665 |
| SchI | GAGTC | 3 cut(s) | 257, 2075, 2416 |
| SdaI | CCTGCAGG | 1 cut(s) | 2665 |
| SduI | GDGCHC | 5 cut(s) | 51, 87, 96, 276, 1288 |
| SfaNI | GCATC | 3 cut(s) | 1528, 1896, 2281 |
| SfcI | CTRYAG | 5 cut(s) | 1172, 1482, 2238, 2661, 2865 |
| SfuI | TTCGAA | 1 cut(s) | 616 |
| SinI | GGWCC | 4 cut(s) | 59, 1527, 2684, 2850 |
| SmaI | CCCGGG | 1 cut(s) | 82 |
| SmiMI | CAYNNNNRTG | 4 cut(s) | 801, 1638, 2652, 2714 |
| SmlI | CTYRAG | 2 cut(s) | 443, 668 |
| SmoI | CTYRAG | 2 cut(s) | 443, 668 |
| SpeI | ACTAGT | 2 cut(s) | 755, 925 |
| Sse8387I | CCTGCAGG | 1 cut(s) | 2665 |
| SsiI | CCGC | 6 cut(s) | 227, 326, 1009, 1999, 2805, 2828 |
| SspMI | CTAG | 8 cut(s) | 468, 756, 890, 926, 1848, 2165, 2184, 2688 |
| SstI | GAGCTC | 1 cut(s) | 96 |
| StyI | CCWWGG | 4 cut(s) | 818, 2142, 2286, 2460 |
| TaaI | ACNGT | 6 cut(s) | 307, 652, 1259, 1463, 2338, 2584 |
| TaiI | ACGT | 3 cut(s) | 907, 1876, 2370 |
| TaqI | TCGA | 6 cut(s) | 160, 286, 616, 1193, 1605, 2955 |
| TatI | WGTACW | 1 cut(s) | 1748 |
| TauI | GCSGC | 3 cut(s) | 328, 1011, 2831 |
| TscAI | CASTG | 4 cut(s) | 924, 1264, 2587, 2974 |
| TseFI | GTSAC | 2 cut(s) | 1207, 1909 |
| TseI | GCWGC | 6 cut(s) | 389, 839, 1027, 1174, 1919, 2867 |
| Tsp45I | GTSAC | 2 cut(s) | 1207, 1909 |
| TspGWI | ACGGA | 3 cut(s) | 65, 248, 2234 |
| TspMI | CCCGGG | 1 cut(s) | 80 |
| TspRI | CASTG | 4 cut(s) | 924, 1264, 2587, 2974 |
| Tth111I | GACNNNGTC | 1 cut(s) | 2345 |
| Van91I | CCANNNNNTGG | 2 cut(s) | 1245, 2681 |
| VneI | GTGCAC | 1 cut(s) | 47 |
| VpaK11BI | GGWCC | 4 cut(s) | 59, 1527, 2684, 2850 |
| XagI | CCTNNNNNAGG | 1 cut(s) | 1730 |
| XapI | RAATTY | 2 cut(s) | 1199, 2310 |
| XceI | RCATGY | 3 cut(s) | 358, 1637, 1884 |
| XmaI | CCCGGG | 1 cut(s) | 80 |
| XspI | CTAG | 8 cut(s) | 468, 756, 890, 926, 1848, 2165, 2184, 2688 |