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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AccB1I | GGYRCC | 4 cut(s) | 118, 641, 1724, 1760 |
| AccB7I | CCANNNNNTGG | 2 cut(s) | 192, 1770 |
| AccBSI | CCGCTC | 3 cut(s) | 1327, 1468, 1872 |
| AccI | GTMKAC | 2 cut(s) | 522, 759 |
| AccII | CGCG | 4 cut(s) | 312, 429, 1122, 1947 |
| AclI | AACGTT | 2 cut(s) | 719, 1455 |
| AclWI | GGATC | 6 cut(s) | 301, 314, 372, 1215, 1234, 1555 |
| AcoI | YGGCCR | 2 cut(s) | 1536, 1653 |
| AcsI | RAATTY | 3 cut(s) | 136, 248, 899 |
| AcuI | CTGAAG | 4 cut(s) | 217, 1229, 1728, 2088 |
| AcyI | GRCGYC | 3 cut(s) | 642, 1437, 1761 |
| AfaI | GTAC | 3 cut(s) | 66, 1691, 1831 |
| AfeI | AGCGCT | 1 cut(s) | 694 |
| AflIII | ACRYGT | 1 cut(s) | 1512 |
| AgsI | TTSAA | 3 cut(s) | 142, 1400, 1862 |
| AhdI | GACNNNNNGTC | 2 cut(s) | 406, 1998 |
| AjiI | CACGTC | 2 cut(s) | 1171, 1795 |
| AjnI | CCWGG | 2 cut(s) | 1175, 1317 |
| Alw21I | GWGCWC | 2 cut(s) | 983, 1335 |
| Alw26I | GTCTC | 4 cut(s) | 779, 1177, 1947, 1985 |
| AlwI | GGATC | 6 cut(s) | 301, 314, 372, 1215, 1234, 1555 |
| AlwNI | CAGNNNCTG | 2 cut(s) | 1087, 1318 |
| Ama87I | CYCGRG | 4 cut(s) | 1074, 1873, 1971, 2010 |
| Aor51HI | AGCGCT | 1 cut(s) | 694 |
| ApeKI | GCWGC | 9 cut(s) | 44, 887, 1058, 1069, 1081, 1522, 1649, 1712, 1798 |
| ApoI | RAATTY | 3 cut(s) | 136, 248, 899 |
| AspLEI | GCGC | 6 cut(s) | 76, 644, 695, 1086, 1763, 1949 |
| AspS9I | GGNCC | 9 cut(s) | 168, 210, 451, 505, 596, 796, 1528, 1642, 1963 |
| AsuC2I | CCSGG | 5 cut(s) | 1075, 1076, 1532, 1972, 1973 |
| AsuHPI | GGTGA | 6 cut(s) | 147, 457, 1237, 1288, 1625, 1786 |
| AsuII | TTCGAA | 1 cut(s) | 438 |
| AvaI | CYCGRG | 4 cut(s) | 1074, 1873, 1971, 2010 |
| AvaII | GGWCC | 5 cut(s) | 168, 210, 451, 796, 1528 |
| BaeGI | GKGCMC | 3 cut(s) | 121, 1026, 1729 |
| BaeI | ACNNNNGTAYC | 2 cut(s) | 708, 741 |
| BamHI | GGATCC | 1 cut(s) | 306 |
| BanI | GGYRCC | 4 cut(s) | 118, 641, 1724, 1760 |
| BanII | GRGCYC | 4 cut(s) | 397, 548, 1335, 1870 |
| BauI | CACGAG | 1 cut(s) | 390 |
| Bbv12I | GWGCWC | 2 cut(s) | 983, 1335 |
| BbvCI | CCTCAGC | 2 cut(s) | 1272, 1635 |
| BbvI | GCAGC | 9 cut(s) | 31, 874, 1070, 1081, 1093, 1509, 1636, 1724, 1810 |
| BccI | CCATC | 6 cut(s) | 186, 556, 680, 995, 1772, 1810 |
| BceAI | ACGGC | 6 cut(s) | 619, 690, 755, 1124, 1244, 1629 |
| BcgI | CGANNNNNNTGC | 6 cut(s) | 752, 786, 866, 900, 1409, 1443 |
| BciT130I | CCWGG | 2 cut(s) | 1177, 1319 |
| BclI | TGATCA | 1 cut(s) | 994 |
| BcnI | CCSGG | 5 cut(s) | 1075, 1076, 1532, 1972, 1973 |
| BcoDI | GTCTC | 4 cut(s) | 779, 1177, 1947, 1985 |
| BfaI | CTAG | 6 cut(s) | 338, 500, 849, 1181, 1607, 1730 |
| BfmI | CTRYAG | 3 cut(s) | 1006, 1355, 1748 |
| BfoI | RGCGCY | 5 cut(s) | 77, 645, 696, 1087, 1764 |
| BglI | GCCNNNNNGGC | 2 cut(s) | 603, 1589 |
| Bme1390I | CCNGG | 7 cut(s) | 1075, 1076, 1177, 1319, 1532, 1972, 1973 |
| Bme18I | GGWCC | 5 cut(s) | 168, 210, 451, 796, 1528 |
| BmeRI | GACNNNNNGTC | 2 cut(s) | 406, 1998 |
| BmeT110I | CYCGRG | 4 cut(s) | 1074, 1873, 1971, 2010 |
| BmgBI | CACGTC | 2 cut(s) | 1171, 1795 |
| BmgT120I | GGNCC | 9 cut(s) | 168, 210, 451, 505, 596, 796, 1528, 1642, 1963 |
| BmrFI | CCNGG | 7 cut(s) | 1075, 1076, 1177, 1319, 1532, 1972, 1973 |
| BmrI | ACTGGG | 3 cut(s) | 1780, 1924, 1992 |
| BmuI | ACTGGG | 3 cut(s) | 1780, 1924, 1992 |
| BoxI | GACNNNNGTC | 1 cut(s) | 518 |
| BplI | GAGNNNNNCTC | 2 cut(s) | 1895, 1927 |
| BpmI | CTGGAG | 5 cut(s) | 696, 986, 1159, 1307, 1523 |
| Bpu10I | CCTNAGC | 4 cut(s) | 1272, 1334, 1377, 1635 |
| Bpu14I | TTCGAA | 1 cut(s) | 438 |
| BpuMI | CCSGG | 5 cut(s) | 1075, 1076, 1532, 1972, 1973 |
| Bsa29I | ATCGAT | 1 cut(s) | 1784 |
| BsaAI | YACGTR | 1 cut(s) | 68 |
| BsaHI | GRCGYC | 3 cut(s) | 642, 1437, 1761 |
| BsaI | GGTCTC | 1 cut(s) | 1985 |
| BsaWI | WCCGGW | 1 cut(s) | 188 |
| BsaXI | ACNNNNNCTCC | 2 cut(s) | 470, 500 |
| Bse118I | RCCGGY | 3 cut(s) | 356, 1538, 1721 |
| Bse1I | ACTGG | 7 cut(s) | 323, 657, 802, 1775, 1930, 1998, 2055 |
| BseBI | CCWGG | 2 cut(s) | 1177, 1319 |
| BseCI | ATCGAT | 1 cut(s) | 1784 |
| BseGI | GGATG | 6 cut(s) | 87, 197, 772, 1156, 1297, 2038 |
| BseMII | CTCAG | 8 cut(s) | 543, 906, 1263, 1348, 1391, 1584, 1626, 1926 |
| BseNI | ACTGG | 7 cut(s) | 323, 657, 802, 1775, 1930, 1998, 2055 |
| BseRI | GAGGAG | 1 cut(s) | 446 |
| BseSI | GKGCMC | 3 cut(s) | 121, 1026, 1729 |
| BseX3I | CGGCCG | 1 cut(s) | 1653 |
| BseXI | GCAGC | 9 cut(s) | 31, 874, 1070, 1081, 1093, 1509, 1636, 1724, 1810 |
| BseYI | CCCAGC | 2 cut(s) | 949, 1949 |
| BsgI | GTGCAG | 3 cut(s) | 30, 881, 1817 |
| Bsh1236I | CGCG | 4 cut(s) | 312, 429, 1122, 1947 |
| Bsh1285I | CGRYCG | 1 cut(s) | 1656 |
| BshNI | GGYRCC | 4 cut(s) | 118, 641, 1724, 1760 |
| BshVI | ATCGAT | 1 cut(s) | 1784 |
| BsiEI | CGRYCG | 1 cut(s) | 1656 |
| BsiHKAI | GWGCWC | 2 cut(s) | 983, 1335 |
| BsiHKCI | CYCGRG | 4 cut(s) | 1074, 1873, 1971, 2010 |
| BsiSI | CCGG | 9 cut(s) | 189, 357, 854, 1075, 1531, 1539, 1722, 1790, 1972 |
| BslFI | GGGAC | 5 cut(s) | 181, 1376, 1501, 1541, 1986 |
| BsmAI | GTCTC | 4 cut(s) | 779, 1177, 1947, 1985 |
| BsmBI | CGTCTC | 1 cut(s) | 1177 |
| BsmFI | GGGAC | 5 cut(s) | 181, 1376, 1501, 1541, 1986 |
| Bso31I | GGTCTC | 1 cut(s) | 1985 |
| BsoBI | CYCGRG | 4 cut(s) | 1074, 1873, 1971, 2010 |
| Bsp119I | TTCGAA | 1 cut(s) | 438 |
| Bsp1286I | GDGCHC | 8 cut(s) | 121, 397, 548, 983, 1026, 1335, 1729, 1870 |
| Bsp143I | GATC | 9 cut(s) | 306, 364, 376, 462, 994, 1207, 1239, 1560, 1596 |
| Bsp19I | CCATGG | 2 cut(s) | 31, 447 |
| BspCNI | CTCAG | 8 cut(s) | 544, 907, 1264, 1347, 1390, 1585, 1627, 1927 |
| BspDI | ATCGAT | 1 cut(s) | 1784 |
| BspFNI | CGCG | 4 cut(s) | 312, 429, 1122, 1947 |
| BspPI | GGATC | 6 cut(s) | 301, 314, 372, 1215, 1234, 1555 |
| BspQI | GCTCTTC | 1 cut(s) | 216 |
| BspT104I | TTCGAA | 1 cut(s) | 438 |
| BspT107I | GGYRCC | 4 cut(s) | 118, 641, 1724, 1760 |
| BspTNI | GGTCTC | 1 cut(s) | 1985 |
| BsrBI | CCGCTC | 3 cut(s) | 1327, 1468, 1872 |
| BsrFI | RCCGGY | 3 cut(s) | 356, 1538, 1721 |
| BsrI | ACTGG | 7 cut(s) | 323, 657, 802, 1775, 1930, 1998, 2055 |
| BssAI | RCCGGY | 3 cut(s) | 356, 1538, 1721 |
| BssMI | GATC | 9 cut(s) | 306, 364, 376, 462, 994, 1207, 1239, 1560, 1596 |
| BssNI | GRCGYC | 3 cut(s) | 642, 1437, 1761 |
| BssSI | CACGAG | 1 cut(s) | 390 |
| BssT1I | CCWWGG | 4 cut(s) | 31, 77, 158, 447 |
| Bst2BI | CACGAG | 1 cut(s) | 390 |
| Bst2UI | CCWGG | 2 cut(s) | 1177, 1319 |
| Bst4CI | ACNGT | 4 cut(s) | 455, 841, 1491, 1987 |
| Bst6I | CTCTTC | 3 cut(s) | 216, 282, 1274 |
| BstACI | GRCGYC | 3 cut(s) | 642, 1437, 1761 |
| BstBAI | YACGTR | 1 cut(s) | 68 |
| BstBI | TTCGAA | 1 cut(s) | 438 |
| BstC8I | GCNNGC | 9 cut(s) | 424, 608, 822, 962, 1120, 1127, 1448, 1540, 1870 |
| BstDSI | CCRYGG | 7 cut(s) | 31, 112, 310, 447, 612, 1120, 1441 |
| BstENI | CCTNNNNNAGG | 2 cut(s) | 162, 1091 |
| BstF5I | GGATG | 6 cut(s) | 87, 197, 772, 1156, 1297, 2038 |
| BstFNI | CGCG | 4 cut(s) | 312, 429, 1122, 1947 |
| BstH2I | RGCGCY | 5 cut(s) | 77, 645, 696, 1087, 1764 |
| BstHHI | GCGC | 6 cut(s) | 76, 644, 695, 1086, 1763, 1949 |
| BstKTI | GATC | 9 cut(s) | 309, 367, 379, 465, 997, 1210, 1242, 1563, 1599 |
| BstMAI | GTCTC | 4 cut(s) | 779, 1177, 1947, 1985 |
| BstMBI | GATC | 9 cut(s) | 306, 364, 376, 462, 994, 1207, 1239, 1560, 1596 |
| BstMCI | CGRYCG | 1 cut(s) | 1656 |
| BstNI | CCWGG | 2 cut(s) | 1177, 1319 |
| BstNSI | RCATGY | 2 cut(s) | 487, 1516 |
| BstPAI | GACNNNNGTC | 1 cut(s) | 518 |
| BstSCI | CCNGG | 7 cut(s) | 1073, 1074, 1175, 1317, 1530, 1970, 1971 |
| BstSFI | CTRYAG | 3 cut(s) | 1006, 1355, 1748 |
| BstSLI | GKGCMC | 3 cut(s) | 121, 1026, 1729 |
| BstUI | CGCG | 4 cut(s) | 312, 429, 1122, 1947 |
| BstV1I | GCAGC | 9 cut(s) | 31, 874, 1070, 1081, 1093, 1509, 1636, 1724, 1810 |
| BstX2I | RGATCY | 4 cut(s) | 306, 364, 1239, 1560 |
| BstXI | CCANNNNNNTGG | 2 cut(s) | 475, 567 |
| BstYI | RGATCY | 4 cut(s) | 306, 364, 1239, 1560 |
| BstZI | CGGCCG | 1 cut(s) | 1653 |
| Bsu15I | ATCGAT | 1 cut(s) | 1784 |
| BsuTUI | ATCGAT | 1 cut(s) | 1784 |
| BtgI | CCRYGG | 7 cut(s) | 31, 112, 310, 447, 612, 1120, 1441 |
| BtgZI | GCGATG | 1 cut(s) | 1440 |
| BtrI | CACGTC | 2 cut(s) | 1171, 1795 |
| BtsCI | GGATG | 6 cut(s) | 87, 197, 772, 1156, 1297, 2038 |
| BtsIMutI | CAGTG | 4 cut(s) | 664, 809, 1700, 2062 |
| Cac8I | GCNNGC | 9 cut(s) | 424, 608, 822, 962, 1120, 1127, 1448, 1540, 1870 |
| CaiI | CAGNNNCTG | 2 cut(s) | 1087, 1318 |
| CciNI | GCGGCCGC | 1 cut(s) | 1653 |
| CfoI | GCGC | 6 cut(s) | 76, 644, 695, 1086, 1763, 1949 |
| Cfr10I | RCCGGY | 3 cut(s) | 356, 1538, 1721 |
| Cfr13I | GGNCC | 9 cut(s) | 168, 210, 451, 505, 596, 796, 1528, 1642, 1963 |
| Cfr42I | CCGCGG | 2 cut(s) | 313, 1123 |
| Cfr9I | CCCGGG | 2 cut(s) | 1074, 1971 |
| ClaI | ATCGAT | 1 cut(s) | 1784 |
| CseI | GACGC | 3 cut(s) | 762, 1413, 1445 |
| Csp6I | GTAC | 3 cut(s) | 65, 1690, 1830 |
| CviAII | CATG | 7 cut(s) | 32, 151, 448, 484, 976, 1043, 1513 |
| CviQI | GTAC | 3 cut(s) | 65, 1690, 1830 |
| DinI | GGCGCC | 2 cut(s) | 643, 1762 |
| DpnI | GATC | 9 cut(s) | 308, 366, 378, 464, 996, 1209, 1241, 1562, 1598 |
| DpnII | GATC | 9 cut(s) | 306, 364, 376, 462, 994, 1207, 1239, 1560, 1596 |
| DriI | GACNNNNNGTC | 2 cut(s) | 406, 1998 |
| EaeI | YGGCCR | 2 cut(s) | 1536, 1653 |
| EagI | CGGCCG | 1 cut(s) | 1653 |
| Eam1104I | CTCTTC | 3 cut(s) | 216, 282, 1274 |
| Eam1105I | GACNNNNNGTC | 2 cut(s) | 406, 1998 |
| EarI | CTCTTC | 3 cut(s) | 216, 282, 1274 |
| EciI | GGCGGA | 5 cut(s) | 51, 788, 1700, 1806, 1991 |
| Ecl136II | GAGCTC | 1 cut(s) | 1333 |
| EclXI | CGGCCG | 1 cut(s) | 1653 |
| Eco130I | CCWWGG | 4 cut(s) | 31, 77, 158, 447 |
| Eco24I | GRGCYC | 4 cut(s) | 397, 548, 1335, 1870 |
| Eco31I | GGTCTC | 1 cut(s) | 1985 |
| Eco47I | GGWCC | 5 cut(s) | 168, 210, 451, 796, 1528 |
| Eco47III | AGCGCT | 1 cut(s) | 694 |
| Eco52I | CGGCCG | 1 cut(s) | 1653 |
| Eco53kI | GAGCTC | 1 cut(s) | 1333 |
| Eco57I | CTGAAG | 4 cut(s) | 217, 1229, 1728, 2088 |
| Eco88I | CYCGRG | 4 cut(s) | 1074, 1873, 1971, 2010 |
| EcoICRI | GAGCTC | 1 cut(s) | 1333 |
| EcoNI | CCTNNNNNAGG | 2 cut(s) | 162, 1091 |
| EcoO109I | RGGNCCY | 1 cut(s) | 168 |
| EcoRI | GAATTC | 2 cut(s) | 248, 899 |
| EcoRII | CCWGG | 2 cut(s) | 1175, 1317 |
| EcoT14I | CCWWGG | 4 cut(s) | 31, 77, 158, 447 |
| EcoT38I | GRGCYC | 4 cut(s) | 397, 548, 1335, 1870 |
| EgeI | GGCGCC | 2 cut(s) | 643, 1762 |
| EheI | GGCGCC | 2 cut(s) | 643, 1762 |
| ErhI | CCWWGG | 4 cut(s) | 31, 77, 158, 447 |
| Esp3I | CGTCTC | 1 cut(s) | 1177 |
| FaeI | CATG | 7 cut(s) | 35, 154, 451, 487, 979, 1046, 1516 |
| FaqI | GGGAC | 5 cut(s) | 181, 1376, 1501, 1541, 1986 |
| FatI | CATG | 7 cut(s) | 31, 150, 447, 483, 975, 1042, 1512 |
| FauNDI | CATATG | 1 cut(s) | 892 |
| FbaI | TGATCA | 1 cut(s) | 994 |
| FblI | GTMKAC | 2 cut(s) | 522, 759 |
| FokI | GGATG | 6 cut(s) | 94, 204, 779, 1163, 1304, 2025 |
| FriOI | GRGCYC | 4 cut(s) | 397, 548, 1335, 1870 |
| FspBI | CTAG | 6 cut(s) | 338, 500, 849, 1181, 1607, 1730 |
| GlaI | GCGC | 6 cut(s) | 75, 643, 694, 1085, 1762, 1948 |
| GsaI | CCCAGC | 2 cut(s) | 953, 1953 |
| GsuI | CTGGAG | 5 cut(s) | 696, 986, 1159, 1307, 1523 |
| HaeII | RGCGCY | 5 cut(s) | 77, 645, 696, 1087, 1764 |
| HapII | CCGG | 9 cut(s) | 189, 357, 854, 1075, 1531, 1539, 1722, 1790, 1972 |
| HgaI | GACGC | 3 cut(s) | 762, 1413, 1445 |
| HhaI | GCGC | 6 cut(s) | 76, 644, 695, 1086, 1763, 1949 |
| Hin1I | GRCGYC | 3 cut(s) | 642, 1437, 1761 |
| Hin1II | CATG | 7 cut(s) | 35, 154, 451, 487, 979, 1046, 1516 |
| Hin6I | GCGC | 6 cut(s) | 74, 642, 693, 1084, 1761, 1947 |
| HinP1I | GCGC | 6 cut(s) | 74, 642, 693, 1084, 1761, 1947 |
| HincII | GTYRAC | 5 cut(s) | 387, 523, 714, 760, 1389 |
| HindII | GTYRAC | 5 cut(s) | 387, 523, 714, 760, 1389 |
| HpaII | CCGG | 9 cut(s) | 189, 357, 854, 1075, 1531, 1539, 1722, 1790, 1972 |
| HphI | GGTGA | 6 cut(s) | 147, 457, 1237, 1288, 1625, 1786 |
| Hpy166II | GTNNAC | 8 cut(s) | 65, 387, 523, 714, 760, 1389, 1895, 2036 |
| Hpy188I | TCNGA | 8 cut(s) | 103, 247, 263, 364, 553, 778, 1936, 2020 |
| Hpy188III | TCNNGA | 5 cut(s) | 203, 235, 904, 1379, 1901 |
| Hpy8I | GTNNAC | 8 cut(s) | 65, 387, 523, 714, 760, 1389, 1895, 2036 |
| Hpy99I | CGWCG | 5 cut(s) | 524, 605, 705, 764, 1407 |
| HpyCH4III | ACNGT | 4 cut(s) | 455, 841, 1491, 1987 |
| HpyCH4IV | ACGT | 5 cut(s) | 67, 719, 1170, 1455, 1794 |
| HpyCH4V | TGCA | 5 cut(s) | 47, 862, 890, 1798, 1983 |
| HpySE526I | ACGT | 5 cut(s) | 67, 719, 1170, 1455, 1794 |
| Hsp92I | GRCGYC | 3 cut(s) | 642, 1437, 1761 |
| Hsp92II | CATG | 7 cut(s) | 35, 154, 451, 487, 979, 1046, 1516 |
| HspAI | GCGC | 6 cut(s) | 74, 642, 693, 1084, 1761, 1947 |
| KasI | GGCGCC | 2 cut(s) | 641, 1760 |
| KroI | GCCGGC | 1 cut(s) | 1538 |
| KroNI | GCCGGC | 1 cut(s) | 1540 |
| Ksp22I | TGATCA | 1 cut(s) | 994 |
| KspI | CCGCGG | 2 cut(s) | 313, 1123 |
| Kzo9I | GATC | 9 cut(s) | 306, 364, 376, 462, 994, 1207, 1239, 1560, 1596 |
| LguI | GCTCTTC | 1 cut(s) | 216 |
| Lsp1109I | GCAGC | 9 cut(s) | 31, 874, 1070, 1081, 1093, 1509, 1636, 1724, 1810 |
| MaeI | CTAG | 6 cut(s) | 338, 500, 849, 1181, 1607, 1730 |
| MaeII | ACGT | 5 cut(s) | 67, 719, 1170, 1455, 1794 |
| MaeIII | GTNAC | 5 cut(s) | 153, 413, 622, 659, 841 |
| MalI | GATC | 9 cut(s) | 308, 366, 378, 464, 996, 1209, 1241, 1562, 1598 |
| MbiI | CCGCTC | 3 cut(s) | 1327, 1468, 1872 |
| MboI | GATC | 9 cut(s) | 306, 364, 376, 462, 994, 1207, 1239, 1560, 1596 |
| MboII | GAAGA | 8 cut(s) | 233, 296, 299, 820, 922, 1240, 1291, 1561 |
| MflI | RGATCY | 4 cut(s) | 306, 364, 1239, 1560 |
| MhlI | GDGCHC | 8 cut(s) | 121, 397, 548, 983, 1026, 1335, 1729, 1870 |
| MluCI | AATT | 4 cut(s) | 136, 248, 331, 899 |
| Mly113I | GGCGCC | 2 cut(s) | 642, 1761 |
| MlyI | GAGTC | 6 cut(s) | 98, 395, 872, 1583, 1676, 1904 |
| MmeI | TCCRAC | 3 cut(s) | 225, 237, 277 |
| MroNI | GCCGGC | 1 cut(s) | 1538 |
| MseI | TTAA | 3 cut(s) | 12, 240, 1263 |
| MspA1I | CMGCKG | 5 cut(s) | 312, 1112, 1122, 1249, 1661 |
| MspI | CCGG | 9 cut(s) | 189, 357, 854, 1075, 1531, 1539, 1722, 1790, 1972 |
| MspR9I | CCNGG | 7 cut(s) | 1075, 1076, 1177, 1319, 1532, 1972, 1973 |
| MvaI | CCWGG | 2 cut(s) | 1177, 1319 |
| MvnI | CGCG | 4 cut(s) | 312, 429, 1122, 1947 |
| NaeI | GCCGGC | 1 cut(s) | 1540 |
| NarI | GGCGCC | 2 cut(s) | 642, 1761 |
| NciI | CCSGG | 5 cut(s) | 1075, 1076, 1532, 1972, 1973 |
| NcoI | CCATGG | 2 cut(s) | 31, 447 |
| NdeI | CATATG | 1 cut(s) | 892 |
| NdeII | GATC | 9 cut(s) | 306, 364, 376, 462, 994, 1207, 1239, 1560, 1596 |
| NgoMIV | GCCGGC | 1 cut(s) | 1538 |
| NlaIII | CATG | 7 cut(s) | 35, 154, 451, 487, 979, 1046, 1516 |
| NmeAIII | GCCGAG | 3 cut(s) | 484, 573, 992 |
| NmuCI | GTSAC | 4 cut(s) | 153, 622, 659, 841 |
| NotI | GCGGCCGC | 1 cut(s) | 1653 |
| NspI | RCATGY | 2 cut(s) | 487, 1516 |
| NspV | TTCGAA | 1 cut(s) | 438 |
| PciI | ACATGT | 1 cut(s) | 1512 |
| PciSI | GCTCTTC | 1 cut(s) | 216 |
| PcsI | WCGNNNNNNNCGW | 2 cut(s) | 609, 759 |
| PdiI | GCCGGC | 1 cut(s) | 1540 |
| PfeI | GAWTC | 4 cut(s) | 98, 146, 972, 1253 |
| PflMI | CCANNNNNTGG | 2 cut(s) | 192, 1770 |
| PleI | GAGTC | 6 cut(s) | 98, 395, 872, 1582, 1675, 1904 |
| PluTI | GGCGCC | 2 cut(s) | 645, 1764 |
| PpsI | GAGTC | 6 cut(s) | 98, 395, 872, 1582, 1675, 1904 |
| Ppu21I | YACGTR | 1 cut(s) | 68 |
| PpuMI | RGGWCCY | 1 cut(s) | 168 |
| PscI | ACATGT | 1 cut(s) | 1512 |
| PshAI | GACNNNNGTC | 1 cut(s) | 518 |
| Psp124BI | GAGCTC | 1 cut(s) | 1335 |
| Psp1406I | AACGTT | 2 cut(s) | 719, 1455 |
| Psp5II | RGGWCCY | 1 cut(s) | 168 |
| Psp6I | CCWGG | 2 cut(s) | 1175, 1317 |
| PspFI | CCCAGC | 2 cut(s) | 949, 1949 |
| PspGI | CCWGG | 2 cut(s) | 1175, 1317 |
| PspPI | GGNCC | 9 cut(s) | 168, 210, 451, 505, 596, 796, 1528, 1642, 1963 |
| PspPPI | RGGWCCY | 1 cut(s) | 168 |
| PsrI | GAACNNNNNNTAC | 2 cut(s) | 333, 365 |
| PstNI | CAGNNNCTG | 2 cut(s) | 1087, 1318 |
| PsuI | RGATCY | 4 cut(s) | 306, 364, 1239, 1560 |
| RsaI | GTAC | 3 cut(s) | 66, 1691, 1831 |
| RsaNI | GTAC | 3 cut(s) | 65, 1690, 1830 |
| SacI | GAGCTC | 1 cut(s) | 1335 |
| SacII | CCGCGG | 2 cut(s) | 313, 1123 |
| SalI | GTCGAC | 2 cut(s) | 521, 758 |
| SapI | GCTCTTC | 1 cut(s) | 216 |
| SaqAI | TTAA | 3 cut(s) | 12, 240, 1263 |
| Sau3AI | GATC | 9 cut(s) | 306, 364, 376, 462, 994, 1207, 1239, 1560, 1596 |
| Sau96I | GGNCC | 9 cut(s) | 168, 210, 451, 505, 596, 796, 1528, 1642, 1963 |
| SchI | GAGTC | 6 cut(s) | 98, 395, 872, 1583, 1676, 1904 |
| ScrFI | CCNGG | 7 cut(s) | 1075, 1076, 1177, 1319, 1532, 1972, 1973 |
| SduI | GDGCHC | 8 cut(s) | 121, 397, 548, 983, 1026, 1335, 1729, 1870 |
| SfcI | CTRYAG | 3 cut(s) | 1006, 1355, 1748 |
| SfoI | GGCGCC | 2 cut(s) | 643, 1762 |
| Sfr303I | CCGCGG | 2 cut(s) | 313, 1123 |
| SfuI | TTCGAA | 1 cut(s) | 438 |
| SgrBI | CCGCGG | 2 cut(s) | 313, 1123 |
| SinI | GGWCC | 5 cut(s) | 168, 210, 451, 796, 1528 |
| SmaI | CCCGGG | 2 cut(s) | 1076, 1973 |
| Sse9I | AATT | 4 cut(s) | 136, 248, 331, 899 |
| SspDI | GGCGCC | 2 cut(s) | 641, 1760 |
| SspMI | CTAG | 6 cut(s) | 338, 500, 849, 1181, 1607, 1730 |
| SstI | GAGCTC | 1 cut(s) | 1335 |
| StyD4I | CCNGG | 7 cut(s) | 1073, 1074, 1175, 1317, 1530, 1970, 1971 |
| StyI | CCWWGG | 4 cut(s) | 31, 77, 158, 447 |
| TaaI | ACNGT | 4 cut(s) | 455, 841, 1491, 1987 |
| TaiI | ACGT | 5 cut(s) | 70, 722, 1173, 1458, 1797 |
| TaqI | TCGA | 7 cut(s) | 375, 438, 522, 759, 876, 1767, 1784 |
| TasI | AATT | 4 cut(s) | 136, 248, 331, 899 |
| TatI | WGTACW | 1 cut(s) | 1689 |
| TfiI | GAWTC | 4 cut(s) | 98, 146, 972, 1253 |
| Tru1I | TTAA | 3 cut(s) | 12, 240, 1263 |
| Tru9I | TTAA | 3 cut(s) | 12, 240, 1263 |
| TscAI | CASTG | 4 cut(s) | 664, 809, 1707, 2062 |
| TseFI | GTSAC | 4 cut(s) | 153, 622, 659, 841 |
| TseI | GCWGC | 9 cut(s) | 44, 887, 1058, 1069, 1081, 1522, 1649, 1712, 1798 |
| Tsp45I | GTSAC | 4 cut(s) | 153, 622, 659, 841 |
| TspDTI | ATGAA | 2 cut(s) | 15, 234 |
| TspGWI | ACGGA | 2 cut(s) | 1220, 1293 |
| TspMI | CCCGGG | 2 cut(s) | 1074, 1971 |
| TspRI | CASTG | 4 cut(s) | 664, 809, 1707, 2062 |
| Van91I | CCANNNNNTGG | 2 cut(s) | 192, 1770 |
| VpaK11BI | GGWCC | 5 cut(s) | 168, 210, 451, 796, 1528 |
| XagI | CCTNNNNNAGG | 2 cut(s) | 162, 1091 |
| XapI | RAATTY | 3 cut(s) | 136, 248, 899 |
| XceI | RCATGY | 2 cut(s) | 487, 1516 |
| XmaI | CCCGGG | 2 cut(s) | 1074, 1971 |
| XmiI | GTMKAC | 2 cut(s) | 522, 759 |
| XspI | CTAG | 6 cut(s) | 338, 500, 849, 1181, 1607, 1730 |