The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH
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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| Acc36I | ACCTGC | 1 cut(s) | 1756 |
| Acc65I | GGTACC | 1 cut(s) | 560 |
| AccB1I | GGYRCC | 3 cut(s) | 34, 441, 560 |
| AccI | GTMKAC | 1 cut(s) | 205 |
| AccII | CGCG | 1 cut(s) | 643 |
| AclWI | GGATC | 5 cut(s) | 110, 469, 618, 944, 1262 |
| AcsI | RAATTY | 1 cut(s) | 1342 |
| AcuI | CTGAAG | 2 cut(s) | 71, 1308 |
| AcyI | GRCGYC | 1 cut(s) | 442 |
| AfaI | GTAC | 5 cut(s) | 41, 253, 562, 862, 1293 |
| AfiI | CCNNNNNNNGG | 5 cut(s) | 374, 398, 570, 571, 1149 |
| AflIII | ACRYGT | 1 cut(s) | 1507 |
| AgeI | ACCGGT | 1 cut(s) | 208 |
| AgsI | TTSAA | 6 cut(s) | 68, 389, 556, 978, 1342, 1666 |
| AhdI | GACNNNNNGTC | 1 cut(s) | 22 |
| AjnI | CCWGG | 2 cut(s) | 1114, 1208 |
| AjuI | GAANNNNNNNTTGG | 2 cut(s) | 1497, 1529 |
| AluBI | AGCT | 5 cut(s) | 249, 292, 794, 1028, 1613 |
| AluI | AGCT | 5 cut(s) | 249, 292, 794, 1028, 1613 |
| Alw21I | GWGCWC | 2 cut(s) | 649, 1182 |
| Alw26I | GTCTC | 2 cut(s) | 132, 1704 |
| AlwI | GGATC | 5 cut(s) | 110, 469, 618, 944, 1262 |
| AlwNI | CAGNNNCTG | 3 cut(s) | 671, 932, 1457 |
| AoxI | GGCC | 6 cut(s) | 122, 364, 376, 635, 667, 1712 |
| ApeKI | GCWGC | 7 cut(s) | 193, 289, 575, 824, 1028, 1772, 1781 |
| ApoI | RAATTY | 1 cut(s) | 1342 |
| ArsI | GACNNNNNNTTYG | 2 cut(s) | 971, 1003 |
| AseI | ATTAAT | 1 cut(s) | 491 |
| AsiGI | ACCGGT | 1 cut(s) | 208 |
| Asp700I | GAANNNNTTC | 1 cut(s) | 1363 |
| Asp718I | GGTACC | 1 cut(s) | 560 |
| AspA2I | CCTAGG | 1 cut(s) | 730 |
| AspLEI | GCGC | 2 cut(s) | 444, 643 |
| AspS9I | GGNCC | 5 cut(s) | 365, 635, 668, 1112, 1712 |
| AsuII | TTCGAA | 1 cut(s) | 969 |
| AvaII | GGWCC | 1 cut(s) | 1112 |
| AvrII | CCTAGG | 1 cut(s) | 730 |
| BaeI | ACNNNNGTAYC | 2 cut(s) | 48, 81 |
| BanI | GGYRCC | 3 cut(s) | 34, 441, 560 |
| BauI | CACGAG | 1 cut(s) | 536 |
| BbsI | GAAGAC | 2 cut(s) | 17, 138 |
| Bbv12I | GWGCWC | 2 cut(s) | 649, 1182 |
| BbvCI | CCTCAGC | 1 cut(s) | 885 |
| BbvI | GCAGC | 7 cut(s) | 205, 301, 562, 836, 1015, 1759, 1768 |
| BccI | CCATC | 6 cut(s) | 67, 73, 706, 1103, 1237, 1390 |
| BceAI | ACGGC | 5 cut(s) | 22, 109, 127, 196, 467 |
| BcgI | CGANNNNNNTGC | 4 cut(s) | 16, 50, 327, 361 |
| BciT130I | CCWGG | 2 cut(s) | 1116, 1210 |
| BciVI | GTATCC | 2 cut(s) | 49, 509 |
| BclI | TGATCA | 2 cut(s) | 673, 1303 |
| BcoDI | GTCTC | 2 cut(s) | 132, 1704 |
| BfaI | CTAG | 6 cut(s) | 120, 162, 653, 731, 1409, 1858 |
| BfmI | CTRYAG | 3 cut(s) | 504, 1479, 1653 |
| BfoI | RGCGCY | 1 cut(s) | 445 |
| BfuAI | ACCTGC | 1 cut(s) | 1756 |
| BfuI | GTATCC | 2 cut(s) | 49, 509 |
| BglI | GCCNNNNNGGC | 1 cut(s) | 1448 |
| BglII | AGATCT | 1 cut(s) | 658 |
| BisI | GCNGC | 9 cut(s) | 194, 197, 261, 290, 576, 825, 1029, 1773, 1782 |
| BlnI | CCTAGG | 1 cut(s) | 730 |
| BlsI | GCNGC | 9 cut(s) | 195, 198, 262, 291, 577, 826, 1030, 1774, 1783 |
| Bme1390I | CCNGG | 2 cut(s) | 1116, 1210 |
| Bme18I | GGWCC | 1 cut(s) | 1112 |
| BmeRI | GACNNNNNGTC | 1 cut(s) | 22 |
| BmgT120I | GGNCC | 5 cut(s) | 365, 635, 668, 1112, 1712 |
| BmiI | GGNNCC | 9 cut(s) | 36, 47, 168, 213, 443, 562, 636, 894, 1713 |
| BmrFI | CCNGG | 2 cut(s) | 1116, 1210 |
| BmsI | GCATC | 2 cut(s) | 1618, 1711 |
| BpiI | GAAGAC | 2 cut(s) | 17, 138 |
| BpmI | CTGGAG | 2 cut(s) | 765, 1137 |
| Bpu10I | CCTNAGC | 1 cut(s) | 885 |
| Bpu14I | TTCGAA | 1 cut(s) | 969 |
| BsaAI | YACGTR | 1 cut(s) | 1510 |
| BsaHI | GRCGYC | 1 cut(s) | 442 |
| BsaJI | CCNNGG | 3 cut(s) | 483, 730, 1715 |
| BsaWI | WCCGGW | 2 cut(s) | 42, 208 |
| Bsc4I | CCNNNNNNNGG | 5 cut(s) | 374, 398, 570, 571, 1149 |
| Bse118I | RCCGGY | 2 cut(s) | 208, 263 |
| Bse1I | ACTGG | 2 cut(s) | 1143, 1653 |
| Bse3DI | GCAATG | 3 cut(s) | 541, 1173, 1425 |
| BseBI | CCWGG | 2 cut(s) | 1116, 1210 |
| BseDI | CCNNGG | 3 cut(s) | 483, 730, 1715 |
| BseGI | GGATG | 9 cut(s) | 84, 88, 717, 726, 1063, 1248, 1401, 1680, 1726 |
| BseLI | CCNNNNNNNGG | 5 cut(s) | 374, 398, 570, 571, 1149 |
| BseMI | GCAATG | 3 cut(s) | 541, 1173, 1425 |
| BseMII | CTCAG | 3 cut(s) | 259, 876, 1605 |
| BseNI | ACTGG | 2 cut(s) | 1143, 1653 |
| BseRI | GAGGAG | 1 cut(s) | 902 |
| BseXI | GCAGC | 7 cut(s) | 205, 301, 562, 836, 1015, 1759, 1768 |
| Bsh1236I | CGCG | 1 cut(s) | 643 |
| BshFI | GGCC | 6 cut(s) | 124, 366, 378, 637, 669, 1714 |
| BshNI | GGYRCC | 3 cut(s) | 34, 441, 560 |
| BshTI | ACCGGT | 1 cut(s) | 208 |
| BsiHKAI | GWGCWC | 2 cut(s) | 649, 1182 |
| BsiSI | CCGG | 3 cut(s) | 43, 209, 264 |
| BslI | CCNNNNNNNGG | 5 cut(s) | 374, 398, 570, 571, 1149 |
| BsmAI | GTCTC | 2 cut(s) | 132, 1704 |
| BsmBI | CGTCTC | 1 cut(s) | 132 |
| BsmI | GAATGC | 2 cut(s) | 1171, 1325 |
| BsnI | GGCC | 6 cut(s) | 124, 366, 378, 637, 669, 1714 |
| Bsp119I | TTCGAA | 1 cut(s) | 969 |
| Bsp1286I | GDGCHC | 2 cut(s) | 649, 1182 |
| Bsp1407I | TGTACA | 1 cut(s) | 860 |
| Bsp19I | CCATGG | 1 cut(s) | 1715 |
| BspANI | GGCC | 6 cut(s) | 124, 366, 378, 637, 669, 1714 |
| BspCNI | CTCAG | 3 cut(s) | 258, 877, 1606 |
| BspFNI | CGCG | 1 cut(s) | 643 |
| BspLI | GGNNCC | 9 cut(s) | 36, 47, 168, 213, 443, 562, 636, 894, 1713 |
| BspMAI | CTGCAG | 1 cut(s) | 508 |
| BspMI | ACCTGC | 1 cut(s) | 1756 |
| BspPI | GGATC | 5 cut(s) | 110, 469, 618, 944, 1262 |
| BspQI | GCTCTTC | 2 cut(s) | 654, 1566 |
| BspT104I | TTCGAA | 1 cut(s) | 969 |
| BspT107I | GGYRCC | 3 cut(s) | 34, 441, 560 |
| BsrDI | GCAATG | 3 cut(s) | 541, 1173, 1425 |
| BsrFI | RCCGGY | 2 cut(s) | 208, 263 |
| BsrGI | TGTACA | 1 cut(s) | 860 |
| BsrI | ACTGG | 2 cut(s) | 1143, 1653 |
| BssAI | RCCGGY | 2 cut(s) | 208, 263 |
| BssECI | CCNNGG | 3 cut(s) | 483, 730, 1715 |
| BssNI | GRCGYC | 1 cut(s) | 442 |
| BssSI | CACGAG | 1 cut(s) | 536 |
| BssT1I | CCWWGG | 2 cut(s) | 730, 1715 |
| Bst2BI | CACGAG | 1 cut(s) | 536 |
| Bst2UI | CCWGG | 2 cut(s) | 1116, 1210 |
| Bst4CI | ACNGT | 4 cut(s) | 256, 628, 1592, 1826 |
| Bst6I | CTCTTC | 2 cut(s) | 654, 1566 |
| BstACI | GRCGYC | 1 cut(s) | 442 |
| BstAPI | GCANNNNNTGC | 2 cut(s) | 1177, 1457 |
| BstAUI | TGTACA | 1 cut(s) | 860 |
| BstBAI | YACGTR | 1 cut(s) | 1510 |
| BstBI | TTCGAA | 1 cut(s) | 969 |
| BstC8I | GCNNGC | 9 cut(s) | 336, 639, 645, 796, 1444, 1453, 1633, 1786, 1805 |
| BstDEI | CTNAG | 3 cut(s) | 245, 885, 1614 |
| BstDSI | CCRYGG | 2 cut(s) | 483, 1715 |
| BstENI | CCTNNNNNAGG | 1 cut(s) | 372 |
| BstF5I | GGATG | 9 cut(s) | 84, 88, 717, 726, 1063, 1248, 1401, 1680, 1726 |
| BstFNI | CGCG | 1 cut(s) | 643 |
| BstH2I | RGCGCY | 1 cut(s) | 445 |
| BstHHI | GCGC | 2 cut(s) | 444, 643 |
| BstMAI | GTCTC | 2 cut(s) | 132, 1704 |
| BstMWI | GCNNNNNNNGC | 9 cut(s) | 295, 653, 1177, 1448, 1452, 1457, 1769, 1778, 1781 |
| BstNI | CCWGG | 2 cut(s) | 1116, 1210 |
| BstNSI | RCATGY | 2 cut(s) | 338, 1001 |
| BstSCI | CCNGG | 2 cut(s) | 1114, 1208 |
| BstSFI | CTRYAG | 3 cut(s) | 504, 1479, 1653 |
| BstUI | CGCG | 1 cut(s) | 643 |
| BstV1I | GCAGC | 7 cut(s) | 205, 301, 562, 836, 1015, 1759, 1768 |
| BstV2I | GAAGAC | 2 cut(s) | 17, 138 |
| BstX2I | RGATCY | 4 cut(s) | 461, 610, 658, 1267 |
| BstYI | RGATCY | 4 cut(s) | 461, 610, 658, 1267 |
| BsuI | GTATCC | 2 cut(s) | 49, 509 |
| BsuRI | GGCC | 6 cut(s) | 124, 366, 378, 637, 669, 1714 |
| BtgI | CCRYGG | 2 cut(s) | 483, 1715 |
| BtsCI | GGATG | 9 cut(s) | 84, 88, 717, 726, 1063, 1248, 1401, 1680, 1726 |
| BtsI | GCAGTG | 4 cut(s) | 846, 900, 1128, 1455 |
| BtsIMutI | CAGTG | 6 cut(s) | 846, 900, 1128, 1182, 1455, 1597 |
| BveI | ACCTGC | 1 cut(s) | 1756 |
| Cac8I | GCNNGC | 9 cut(s) | 336, 639, 645, 796, 1444, 1453, 1633, 1786, 1805 |
| CaiI | CAGNNNCTG | 3 cut(s) | 671, 932, 1457 |
| CfoI | GCGC | 2 cut(s) | 444, 643 |
| Cfr10I | RCCGGY | 2 cut(s) | 208, 263 |
| Cfr13I | GGNCC | 5 cut(s) | 365, 635, 668, 1112, 1712 |
| Csp6I | GTAC | 5 cut(s) | 40, 252, 561, 861, 1292 |
| CspAI | ACCGGT | 1 cut(s) | 208 |
| CviAII | CATG | 8 cut(s) | 335, 708, 916, 998, 1069, 1262, 1447, 1716 |
| CviQI | GTAC | 5 cut(s) | 40, 252, 561, 861, 1292 |
| DdeI | CTNAG | 3 cut(s) | 245, 885, 1614 |
| DinI | GGCGCC | 1 cut(s) | 443 |
| DraI | TTTAAA | 1 cut(s) | 426 |
| DriI | GACNNNNNGTC | 1 cut(s) | 22 |
| Eam1104I | CTCTTC | 2 cut(s) | 654, 1566 |
| Eam1105I | GACNNNNNGTC | 1 cut(s) | 22 |
| EarI | CTCTTC | 2 cut(s) | 654, 1566 |
| Eco130I | CCWWGG | 2 cut(s) | 730, 1715 |
| Eco147I | AGGCCT | 1 cut(s) | 378 |
| Eco32I | GATATC | 1 cut(s) | 1476 |
| Eco47I | GGWCC | 1 cut(s) | 1112 |
| Eco57I | CTGAAG | 2 cut(s) | 71, 1308 |
| EcoNI | CCTNNNNNAGG | 1 cut(s) | 372 |
| EcoO109I | RGGNCCY | 1 cut(s) | 668 |
| EcoRI | GAATTC | 1 cut(s) | 1342 |
| EcoRII | CCWGG | 2 cut(s) | 1114, 1208 |
| EcoRV | GATATC | 1 cut(s) | 1476 |
| EcoT14I | CCWWGG | 2 cut(s) | 730, 1715 |
| EcoT22I | ATGCAT | 3 cut(s) | 340, 999, 1173 |
| EgeI | GGCGCC | 1 cut(s) | 443 |
| EheI | GGCGCC | 1 cut(s) | 443 |
| ErhI | CCWWGG | 2 cut(s) | 730, 1715 |
| Esp3I | CGTCTC | 1 cut(s) | 132 |
| FaeI | CATG | 8 cut(s) | 338, 711, 919, 1001, 1072, 1265, 1450, 1719 |
| FalI | AAGNNNNNCTT | 2 cut(s) | 562, 594 |
| FatI | CATG | 8 cut(s) | 334, 707, 915, 997, 1068, 1261, 1446, 1715 |
| FauI | CCCGC | 3 cut(s) | 1171, 1279, 1702 |
| FbaI | TGATCA | 2 cut(s) | 673, 1303 |
| FblI | GTMKAC | 1 cut(s) | 205 |
| Fnu4HI | GCNGC | 9 cut(s) | 194, 197, 261, 290, 576, 825, 1029, 1773, 1782 |
| FokI | GGATG | 9 cut(s) | 91, 95, 713, 724, 1050, 1255, 1408, 1667, 1733 |
| Fsp4HI | GCNGC | 9 cut(s) | 194, 197, 261, 290, 576, 825, 1029, 1773, 1782 |
| FspBI | CTAG | 6 cut(s) | 120, 162, 653, 731, 1409, 1858 |
| GlaI | GCGC | 2 cut(s) | 443, 642 |
| GluI | GCNGC | 9 cut(s) | 194, 197, 261, 290, 576, 825, 1029, 1773, 1782 |
| GsuI | CTGGAG | 2 cut(s) | 765, 1137 |
| HaeII | RGCGCY | 1 cut(s) | 445 |
| HaeIII | GGCC | 6 cut(s) | 124, 366, 378, 637, 669, 1714 |
| HapII | CCGG | 3 cut(s) | 43, 209, 264 |
| HhaI | GCGC | 2 cut(s) | 444, 643 |
| Hin1I | GRCGYC | 1 cut(s) | 442 |
| Hin1II | CATG | 8 cut(s) | 338, 711, 919, 1001, 1072, 1265, 1450, 1719 |
| Hin6I | GCGC | 2 cut(s) | 442, 641 |
| HinP1I | GCGC | 2 cut(s) | 442, 641 |
| HincII | GTYRAC | 1 cut(s) | 1620 |
| HindII | GTYRAC | 1 cut(s) | 1620 |
| HindIII | AAGCTT | 1 cut(s) | 792 |
| HinfI | GANTC | 6 cut(s) | 17, 28, 202, 235, 929, 1666 |
| HpaII | CCGG | 3 cut(s) | 43, 209, 264 |
| Hpy166II | GTNNAC | 5 cut(s) | 206, 863, 1294, 1620, 1640 |
| Hpy188III | TCNNGA | 1 cut(s) | 469 |
| Hpy8I | GTNNAC | 5 cut(s) | 206, 863, 1294, 1620, 1640 |
| Hpy99I | CGWCG | 3 cut(s) | 136, 154, 157 |
| HpyAV | CCTTC | 4 cut(s) | 46, 432, 457, 562 |
| HpyCH4III | ACNGT | 4 cut(s) | 256, 628, 1592, 1826 |
| HpyCH4IV | ACGT | 2 cut(s) | 679, 1509 |
| HpyF10VI | GCNNNNNNNGC | 9 cut(s) | 295, 653, 1177, 1448, 1452, 1457, 1769, 1778, 1781 |
| HpyF3I | CTNAG | 3 cut(s) | 245, 885, 1614 |
| HpySE526I | ACGT | 2 cut(s) | 679, 1509 |
| Hsp92I | GRCGYC | 1 cut(s) | 442 |
| Hsp92II | CATG | 8 cut(s) | 338, 711, 919, 1001, 1072, 1265, 1450, 1719 |
| HspAI | GCGC | 2 cut(s) | 442, 641 |
| KasI | GGCGCC | 1 cut(s) | 441 |
| KpnI | GGTACC | 1 cut(s) | 564 |
| Ksp22I | TGATCA | 2 cut(s) | 673, 1303 |
| LguI | GCTCTTC | 2 cut(s) | 654, 1566 |
| LmnI | GCTCC | 3 cut(s) | 746, 940, 1118 |
| Lsp1109I | GCAGC | 7 cut(s) | 205, 301, 562, 836, 1015, 1759, 1768 |
| LweI | GCATC | 2 cut(s) | 1618, 1711 |
| MaeI | CTAG | 6 cut(s) | 120, 162, 653, 731, 1409, 1858 |
| MaeII | ACGT | 2 cut(s) | 679, 1509 |
| MaeIII | GTNAC | 5 cut(s) | 410, 680, 722, 868, 1606 |
| MboII | GAAGA | 7 cut(s) | 22, 138, 179, 336, 447, 641, 1553 |
| MfeI | CAATTG | 1 cut(s) | 1674 |
| MflI | RGATCY | 4 cut(s) | 461, 610, 658, 1267 |
| MhlI | GDGCHC | 2 cut(s) | 649, 1182 |
| Mly113I | GGCGCC | 1 cut(s) | 442 |
| MlyI | GAGTC | 3 cut(s) | 11, 211, 229 |
| MmeI | TCCRAC | 1 cut(s) | 1451 |
| MnlI | CCTC | 9 cut(s) | 102, 119, 880, 883, 1075, 1242, 1511, 1584, 1730 |
| Mph1103I | ATGCAT | 3 cut(s) | 340, 999, 1173 |
| MroXI | GAANNNNTTC | 1 cut(s) | 1363 |
| MseI | TTAA | 7 cut(s) | 302, 425, 491, 819, 983, 1104, 1148 |
| MslI | CAYNNNNRTG | 3 cut(s) | 230, 1187, 1299 |
| MspA1I | CMGCKG | 2 cut(s) | 249, 1613 |
| MspI | CCGG | 3 cut(s) | 43, 209, 264 |
| MspR9I | CCNGG | 2 cut(s) | 1116, 1210 |
| MunI | CAATTG | 1 cut(s) | 1674 |
| Mva1269I | GAATGC | 2 cut(s) | 1171, 1325 |
| MvaI | CCWGG | 2 cut(s) | 1116, 1210 |
| MvnI | CGCG | 1 cut(s) | 643 |
| MwoI | GCNNNNNNNGC | 9 cut(s) | 295, 653, 1177, 1448, 1452, 1457, 1769, 1778, 1781 |
| NarI | GGCGCC | 1 cut(s) | 442 |
| NcoI | CCATGG | 1 cut(s) | 1715 |
| NlaIII | CATG | 8 cut(s) | 338, 711, 919, 1001, 1072, 1265, 1450, 1719 |
| NlaIV | GGNNCC | 9 cut(s) | 36, 47, 168, 213, 443, 562, 636, 894, 1713 |
| NmuCI | GTSAC | 1 cut(s) | 410 |
| NsiI | ATGCAT | 3 cut(s) | 340, 999, 1173 |
| NspI | RCATGY | 2 cut(s) | 338, 1001 |
| NspV | TTCGAA | 1 cut(s) | 969 |
| PaeI | GCATGC | 1 cut(s) | 338 |
| PceI | AGGCCT | 1 cut(s) | 378 |
| PciSI | GCTCTTC | 2 cut(s) | 654, 1566 |
| PcsI | WCGNNNNNNNCGW | 3 cut(s) | 140, 146, 180 |
| PctI | GAATGC | 2 cut(s) | 1171, 1325 |
| PdmI | GAANNNNTTC | 1 cut(s) | 1363 |
| PfeI | GAWTC | 3 cut(s) | 28, 929, 1666 |
| PfoI | TCCNGGA | 1 cut(s) | 1114 |
| PinAI | ACCGGT | 1 cut(s) | 208 |
| PkrI | GCNGC | 9 cut(s) | 195, 198, 262, 291, 577, 826, 1030, 1774, 1783 |
| PleI | GAGTC | 3 cut(s) | 11, 210, 229 |
| PluTI | GGCGCC | 1 cut(s) | 445 |
| PpsI | GAGTC | 3 cut(s) | 11, 210, 229 |
| Ppu21I | YACGTR | 1 cut(s) | 1510 |
| PshBI | ATTAAT | 1 cut(s) | 491 |
| Psp6I | CCWGG | 2 cut(s) | 1114, 1208 |
| PspGI | CCWGG | 2 cut(s) | 1114, 1208 |
| PspN4I | GGNNCC | 9 cut(s) | 36, 47, 168, 213, 443, 562, 636, 894, 1713 |
| PspPI | GGNCC | 5 cut(s) | 365, 635, 668, 1112, 1712 |
| PstI | CTGCAG | 1 cut(s) | 508 |
| PstNI | CAGNNNCTG | 3 cut(s) | 671, 932, 1457 |
| PsuI | RGATCY | 4 cut(s) | 461, 610, 658, 1267 |
| PvuII | CAGCTG | 2 cut(s) | 249, 1613 |
| RsaI | GTAC | 5 cut(s) | 41, 253, 562, 862, 1293 |
| RsaNI | GTAC | 5 cut(s) | 40, 252, 561, 861, 1292 |
| RseI | CAYNNNNRTG | 3 cut(s) | 230, 1187, 1299 |
| SapI | GCTCTTC | 2 cut(s) | 654, 1566 |
| SaqAI | TTAA | 7 cut(s) | 302, 425, 491, 819, 983, 1104, 1148 |
| SatI | GCNGC | 9 cut(s) | 194, 197, 261, 290, 576, 825, 1029, 1773, 1782 |
| Sau96I | GGNCC | 5 cut(s) | 365, 635, 668, 1112, 1712 |
| SchI | GAGTC | 3 cut(s) | 11, 211, 229 |
| ScrFI | CCNGG | 2 cut(s) | 1116, 1210 |
| SduI | GDGCHC | 2 cut(s) | 649, 1182 |
| SfaNI | GCATC | 2 cut(s) | 1618, 1711 |
| SfcI | CTRYAG | 3 cut(s) | 504, 1479, 1653 |
| SfoI | GGCGCC | 1 cut(s) | 443 |
| SfuI | TTCGAA | 1 cut(s) | 969 |
| SgrAI | CRCCGGYG | 1 cut(s) | 263 |
| SinI | GGWCC | 1 cut(s) | 1112 |
| SmiMI | CAYNNNNRTG | 3 cut(s) | 230, 1187, 1299 |
| SphI | GCATGC | 1 cut(s) | 338 |
| SseBI | AGGCCT | 1 cut(s) | 378 |
| SspDI | GGCGCC | 1 cut(s) | 441 |
| SspMI | CTAG | 6 cut(s) | 120, 162, 653, 731, 1409, 1858 |
| StuI | AGGCCT | 1 cut(s) | 378 |
| StyD4I | CCNGG | 2 cut(s) | 1114, 1208 |
| StyI | CCWWGG | 2 cut(s) | 730, 1715 |
| TaaI | ACNGT | 4 cut(s) | 256, 628, 1592, 1826 |
| TaiI | ACGT | 2 cut(s) | 682, 1512 |
| TaqI | TCGA | 4 cut(s) | 26, 105, 969, 1838 |
| TaqII | GACCGA | 1 cut(s) | 29 |
| TatI | WGTACW | 2 cut(s) | 860, 1291 |
| TauI | GCSGC | 2 cut(s) | 199, 263 |
| TfiI | GAWTC | 3 cut(s) | 28, 929, 1666 |
| Tru1I | TTAA | 7 cut(s) | 302, 425, 491, 819, 983, 1104, 1148 |
| Tru9I | TTAA | 7 cut(s) | 302, 425, 491, 819, 983, 1104, 1148 |
| TscAI | CASTG | 6 cut(s) | 846, 907, 1128, 1182, 1462, 1597 |
| TseFI | GTSAC | 1 cut(s) | 410 |
| TseI | GCWGC | 7 cut(s) | 193, 289, 575, 824, 1028, 1772, 1781 |
| Tsp45I | GTSAC | 1 cut(s) | 410 |
| TspDTI | ATGAA | 3 cut(s) | 439, 1056, 1838 |
| TspGWI | ACGGA | 4 cut(s) | 74, 120, 1206, 1250 |
| TspRI | CASTG | 6 cut(s) | 846, 907, 1128, 1182, 1462, 1597 |
| VpaK11BI | GGWCC | 1 cut(s) | 1112 |
| VspI | ATTAAT | 1 cut(s) | 491 |
| XagI | CCTNNNNNAGG | 1 cut(s) | 372 |
| XapI | RAATTY | 1 cut(s) | 1342 |
| XceI | RCATGY | 2 cut(s) | 338, 1001 |
| XmaJI | CCTAGG | 1 cut(s) | 730 |
| XmiI | GTMKAC | 1 cut(s) | 205 |
| XmnI | GAANNNNTTC | 1 cut(s) | 1363 |
| XspI | CTAG | 6 cut(s) | 120, 162, 653, 731, 1409, 1858 |
| Zsp2I | ATGCAT | 3 cut(s) | 340, 999, 1173 |