gag-polypeptide of LTR copia-type
| Domain Name | Pfam ID | Position | E-value | Description |
|---|---|---|---|---|
| DUF4219 | PF13961 | 179 - 205 | 2.7e-09 | Domain of unknown function (DUF4219) |
| Retrotran_gag_2 | PF14223 | 191 - 371 | 1e-35 | gag-polypeptide of LTR copia-type |
| Pol_BBD | PF22936 | 490 - 570 | 7.3e-28 | Pol polyprotein, beta-barrel domain |
| gag_pre-integrs | PF13976 | 603 - 665 | 3.2e-16 | GAG-pre-integrase domain |
| rve | PF00665 | 679 - 780 | 3e-15 | Integrase core domain |
| SH3_retrovirus | PF25597 | 854 - 915 | 3.4e-26 | Retroviral polymerase SH3-like domain |
| RVT_2 | PF07727 | 1031 - 1199 | 2.3e-65 | Reverse transcriptase (RNA-dependent DNA polymerase) |
| mTERF | PF02536 | 1212 - 1432 | 3.4e-45 | mTERF |
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) |
|---|---|---|---|
| AarI | CACCTGC | 1 cut(s) | 2854 |
| Acc36I | ACCTGC | 1 cut(s) | 2854 |
| AccB1I | GGYRCC | 1 cut(s) | 1484 |
| AccB7I | CCANNNNNTGG | 1 cut(s) | 2681 |
| AccI | GTMKAC | 7 cut(s) | 1647, 2021, 2314, 2457, 2941, 3018, 3381 |
| AccII | CGCG | 1 cut(s) | 1218 |
| AclI | AACGTT | 1 cut(s) | 1551 |
| AclWI | GGATC | 4 cut(s) | 2328, 4064, 4166, 4179 |
| AcoI | YGGCCR | 1 cut(s) | 1207 |
| AcuI | CTGAAG | 6 cut(s) | 2180, 3455, 3461, 3623, 3798, 4197 |
| AcyI | GRCGYC | 1 cut(s) | 1485 |
| AdeI | CACNNNGTG | 1 cut(s) | 3528 |
| AfeI | AGCGCT | 2 cut(s) | 1317, 4071 |
| AfiI | CCNNNNNNNGG | 8 cut(s) | 151, 667, 1586, 2386, 2681, 2750, 3456, 3764 |
| AflII | CTTAAG | 2 cut(s) | 1835, 4163 |
| AflIII | ACRYGT | 2 cut(s) | 1497, 2575 |
| AhdI | GACNNNNNGTC | 1 cut(s) | 3866 |
| AhlI | ACTAGT | 1 cut(s) | 3205 |
| AjiI | CACGTC | 3 cut(s) | 1223, 1241, 2707 |
| AjnI | CCWGG | 2 cut(s) | 2144, 2530 |
| AjuI | GAANNNNNNNTTGG | 8 cut(s) | 566, 598, 2721, 2753, 3947, 3979, 4245, 4277 |
| AleI | CACNNNNGTG | 2 cut(s) | 1500, 2063 |
| Alw21I | GWGCWC | 6 cut(s) | 537, 592, 1011, 1360, 1530, 2052 |
| Alw26I | GTCTC | 9 cut(s) | 254, 687, 757, 1025, 1557, 2697, 2999, 3196, 4010 |
| AlwI | GGATC | 4 cut(s) | 2328, 4064, 4166, 4179 |
| Ama87I | CYCGRG | 1 cut(s) | 3795 |
| Aor51HI | AGCGCT | 2 cut(s) | 1317, 4071 |
| AoxI | GGCC | 5 cut(s) | 576, 1207, 2740, 3755, 4006 |
| ApeKI | GCWGC | 4 cut(s) | 515, 1126, 3305, 4111 |
| ArsI | GACNNNNNNTTYG | 8 cut(s) | 103, 135, 725, 757, 986, 1018, 2696, 2728 |
| AseI | ATTAAT | 2 cut(s) | 1634, 1763 |
| Asp700I | GAANNNNTTC | 2 cut(s) | 4257, 4276 |
| AspA2I | CCTAGG | 1 cut(s) | 3848 |
| AspLEI | GCGC | 4 cut(s) | 1318, 1487, 3472, 4072 |
| AspS9I | GGNCC | 5 cut(s) | 577, 994, 2072, 2741, 3860 |
| AsuHPI | GGTGA | 9 cut(s) | 81, 863, 956, 1619, 1942, 2704, 2844, 2871, 3514 |
| AsuII | TTCGAA | 1 cut(s) | 858 |
| AvaI | CYCGRG | 1 cut(s) | 3795 |
| AvaII | GGWCC | 3 cut(s) | 994, 2072, 3860 |
| AvrII | CCTAGG | 1 cut(s) | 3848 |
| AxyI | CCTNAGG | 1 cut(s) | 2421 |
| BaeGI | GKGCMC | 2 cut(s) | 1659, 3533 |
| BaeI | ACNNNNGTAYC | 2 cut(s) | 3707, 3740 |
| BamHI | GGATCC | 1 cut(s) | 4171 |
| BanI | GGYRCC | 1 cut(s) | 1484 |
| BanII | GRGCYC | 5 cut(s) | 1076, 1360, 1530, 2035, 2052 |
| BarI | GAAGNNNNNNTAC | 4 cut(s) | 692, 724, 1965, 1997 |
| BauI | CACGAG | 1 cut(s) | 4188 |
| BbsI | GAAGAC | 4 cut(s) | 827, 2693, 3429, 4125 |
| Bbv12I | GWGCWC | 6 cut(s) | 537, 592, 1011, 1360, 1530, 2052 |
| BbvI | GCAGC | 4 cut(s) | 527, 1138, 3317, 4098 |
| BccI | CCATC | 9 cut(s) | 41, 1442, 1921, 2797, 3143, 3403, 3665, 3859, 4162 |
| BceAI | ACGGC | 3 cut(s) | 902, 2189, 3904 |
| BcgI | CGANNNNNNTGC | 4 cut(s) | 3271, 3305, 3853, 3887 |
| BciT130I | CCWGG | 2 cut(s) | 2146, 2532 |
| BciVI | GTATCC | 2 cut(s) | 3802, 3888 |
| BclI | TGATCA | 2 cut(s) | 1960, 2694 |
| BcoDI | GTCTC | 9 cut(s) | 254, 687, 757, 1025, 1557, 2697, 2999, 3196, 4010 |
| BcuI | ACTAGT | 1 cut(s) | 3205 |
| BfaI | CTAG | 5 cut(s) | 1430, 3206, 3849, 3969, 4010 |
| BfmI | CTRYAG | 1 cut(s) | 3220 |
| BfoI | RGCGCY | 4 cut(s) | 1319, 1488, 3473, 4073 |
| BfrI | CTTAAG | 2 cut(s) | 1835, 4163 |
| BfuAI | ACCTGC | 1 cut(s) | 2854 |
| BfuI | GTATCC | 2 cut(s) | 3802, 3888 |
| BglII | AGATCT | 3 cut(s) | 2246, 2755, 2947 |
| BisI | GCNGC | 5 cut(s) | 516, 1127, 3306, 4112, 4208 |
| BlnI | CCTAGG | 1 cut(s) | 3848 |
| BlsI | GCNGC | 5 cut(s) | 517, 1128, 3307, 4113, 4209 |
| BmcAI | AGTACT | 2 cut(s) | 3503, 3811 |
| Bme1390I | CCNGG | 2 cut(s) | 2146, 2532 |
| Bme18I | GGWCC | 3 cut(s) | 994, 2072, 3860 |
| BmeRI | GACNNNNNGTC | 1 cut(s) | 3866 |
| BmeT110I | CYCGRG | 1 cut(s) | 3795 |
| BmgBI | CACGTC | 3 cut(s) | 1223, 1241, 2707 |
| BmgT120I | GGNCC | 5 cut(s) | 577, 994, 2072, 2741, 3860 |
| BmiI | GGNNCC | 5 cut(s) | 811, 996, 1486, 2906, 4173 |
| BmrFI | CCNGG | 2 cut(s) | 2146, 2532 |
| BmrI | ACTGGG | 1 cut(s) | 175 |
| BmsI | GCATC | 6 cut(s) | 1879, 1894, 1956, 2894, 3501, 4194 |
| BmuI | ACTGGG | 1 cut(s) | 175 |
| BpiI | GAAGAC | 4 cut(s) | 827, 2693, 3429, 4125 |
| BplI | GAGNNNNNCTC | 4 cut(s) | 737, 769, 2586, 2618 |
| Bpu14I | TTCGAA | 1 cut(s) | 858 |
| BpuEI | CTTGAG | 5 cut(s) | 739, 889, 1118, 1346, 2066 |
| Bsa29I | ATCGAT | 1 cut(s) | 2470 |
| BsaAI | YACGTR | 1 cut(s) | 1654 |
| BsaBI | GATNNNNATC | 2 cut(s) | 443, 1452 |
| BsaHI | GRCGYC | 1 cut(s) | 1485 |
| BsaI | GGTCTC | 1 cut(s) | 757 |
| BsaJI | CCNNGG | 6 cut(s) | 495, 1210, 1770, 2145, 3796, 3848 |
| Bsc4I | CCNNNNNNNGG | 8 cut(s) | 151, 667, 1586, 2386, 2681, 2750, 3456, 3764 |
| Bse118I | RCCGGY | 2 cut(s) | 1481, 4246 |
| Bse1I | ACTGG | 3 cut(s) | 181, 530, 3014 |
| Bse21I | CCTNAGG | 1 cut(s) | 2421 |
| Bse3DI | GCAATG | 1 cut(s) | 3066 |
| Bse8I | GATNNNNATC | 2 cut(s) | 443, 1452 |
| BseBI | CCWGG | 2 cut(s) | 2146, 2532 |
| BseCI | ATCGAT | 1 cut(s) | 2470 |
| BseDI | CCNNGG | 6 cut(s) | 495, 1210, 1770, 2145, 3796, 3848 |
| BseGI | GGATG | 8 cut(s) | 33, 1599, 1800, 1982, 3070, 3343, 3698, 3978 |
| BseJI | GATNNNNATC | 2 cut(s) | 443, 1452 |
| BseLI | CCNNNNNNNGG | 8 cut(s) | 151, 667, 1586, 2386, 2681, 2750, 3456, 3764 |
| BseMI | GCAATG | 1 cut(s) | 3066 |
| BseMII | CTCAG | 6 cut(s) | 31, 618, 3621, 3743, 4103, 4272 |
| BseNI | ACTGG | 3 cut(s) | 181, 530, 3014 |
| BseRI | GAGGAG | 5 cut(s) | 1299, 2271, 2274, 2605, 4028 |
| BseSI | GKGCMC | 2 cut(s) | 1659, 3533 |
| BseXI | GCAGC | 4 cut(s) | 527, 1138, 3317, 4098 |
| Bsh1236I | CGCG | 1 cut(s) | 1218 |
| BshFI | GGCC | 5 cut(s) | 578, 1209, 2742, 3757, 4008 |
| BshNI | GGYRCC | 1 cut(s) | 1484 |
| BshVI | ATCGAT | 1 cut(s) | 2470 |
| BsiHKAI | GWGCWC | 6 cut(s) | 537, 592, 1011, 1360, 1530, 2052 |
| BsiHKCI | CYCGRG | 1 cut(s) | 3795 |
| BsiSI | CCGG | 3 cut(s) | 1482, 3234, 4247 |
| BslFI | GGGAC | 5 cut(s) | 105, 637, 2812, 3814, 3919 |
| BslI | CCNNNNNNNGG | 8 cut(s) | 151, 667, 1586, 2386, 2681, 2750, 3456, 3764 |
| BsmAI | GTCTC | 9 cut(s) | 254, 687, 757, 1025, 1557, 2697, 2999, 3196, 4010 |
| BsmBI | CGTCTC | 2 cut(s) | 1557, 2697 |
| BsmFI | GGGAC | 5 cut(s) | 105, 637, 2812, 3814, 3919 |
| BsmI | GAATGC | 2 cut(s) | 300, 2186 |
| BsnI | GGCC | 5 cut(s) | 578, 1209, 2742, 3757, 4008 |
| Bso31I | GGTCTC | 1 cut(s) | 757 |
| BsoBI | CYCGRG | 1 cut(s) | 3795 |
| Bsp119I | TTCGAA | 1 cut(s) | 858 |
| Bsp1407I | TGTACA | 2 cut(s) | 2572, 3153 |
| Bsp19I | CCATGG | 1 cut(s) | 495 |
| BspANI | GGCC | 5 cut(s) | 578, 1209, 2742, 3757, 4008 |
| BspCNI | CTCAG | 6 cut(s) | 30, 619, 3622, 3744, 4102, 4273 |
| BspDI | ATCGAT | 1 cut(s) | 2470 |
| BspFNI | CGCG | 1 cut(s) | 1218 |
| BspHI | TCATGA | 2 cut(s) | 3535, 3615 |
| BspLI | GGNNCC | 5 cut(s) | 811, 996, 1486, 2906, 4173 |
| BspMI | ACCTGC | 1 cut(s) | 2854 |
| BspPI | GGATC | 4 cut(s) | 2328, 4064, 4166, 4179 |
| BspT104I | TTCGAA | 1 cut(s) | 858 |
| BspT107I | GGYRCC | 1 cut(s) | 1484 |
| BspTI | CTTAAG | 2 cut(s) | 1835, 4163 |
| BspTNI | GGTCTC | 1 cut(s) | 757 |
| BsrDI | GCAATG | 1 cut(s) | 3066 |
| BsrFI | RCCGGY | 2 cut(s) | 1481, 4246 |
| BsrGI | TGTACA | 2 cut(s) | 2572, 3153 |
| BsrI | ACTGG | 3 cut(s) | 181, 530, 3014 |
| BssAI | RCCGGY | 2 cut(s) | 1481, 4246 |
| BssECI | CCNNGG | 6 cut(s) | 495, 1210, 1770, 2145, 3796, 3848 |
| BssNAI | GTATAC | 1 cut(s) | 2942 |
| BssNI | GRCGYC | 1 cut(s) | 1485 |
| BssSI | CACGAG | 1 cut(s) | 4188 |
| BssT1I | CCWWGG | 3 cut(s) | 495, 1770, 3848 |
| Bst1107I | GTATAC | 1 cut(s) | 2942 |
| Bst2BI | CACGAG | 1 cut(s) | 4188 |
| Bst2UI | CCWGG | 2 cut(s) | 2146, 2532 |
| Bst4CI | ACNGT | 8 cut(s) | 944, 1944, 2326, 2692, 3112, 3910, 4021, 4308 |
| Bst6I | CTCTTC | 6 cut(s) | 1023, 1086, 1100, 1404, 2123, 2778 |
| BstACI | GRCGYC | 1 cut(s) | 1485 |
| BstAFI | CTTAAG | 2 cut(s) | 1835, 4163 |
| BstAPI | GCANNNNNTGC | 1 cut(s) | 3266 |
| BstAUI | TGTACA | 2 cut(s) | 2572, 3153 |
| BstBAI | YACGTR | 1 cut(s) | 1654 |
| BstBI | TTCGAA | 1 cut(s) | 858 |
| BstC8I | GCNNGC | 9 cut(s) | 777, 1076, 1435, 1489, 2744, 2748, 2811, 3950, 4074 |
| BstDSI | CCRYGG | 1 cut(s) | 495 |
| BstEII | GGTNACC | 1 cut(s) | 1625 |
| BstF5I | GGATG | 8 cut(s) | 33, 1599, 1800, 1982, 3070, 3343, 3698, 3978 |
| BstFNI | CGCG | 1 cut(s) | 1218 |
| BstH2I | RGCGCY | 4 cut(s) | 1319, 1488, 3473, 4073 |
| BstHHI | GCGC | 4 cut(s) | 1318, 1487, 3472, 4072 |
| BstMAI | GTCTC | 9 cut(s) | 254, 687, 757, 1025, 1557, 2697, 2999, 3196, 4010 |
| BstNI | CCWGG | 2 cut(s) | 2146, 2532 |
| BstNSI | RCATGY | 7 cut(s) | 1145, 1437, 1501, 2451, 2579, 2750, 3545 |
| BstPI | GGTNACC | 1 cut(s) | 1625 |
| BstSCI | CCNGG | 2 cut(s) | 2144, 2530 |
| BstSFI | CTRYAG | 1 cut(s) | 3220 |
| BstSLI | GKGCMC | 2 cut(s) | 1659, 3533 |
| BstUI | CGCG | 1 cut(s) | 1218 |
| BstV1I | GCAGC | 4 cut(s) | 527, 1138, 3317, 4098 |
| BstV2I | GAAGAC | 4 cut(s) | 827, 2693, 3429, 4125 |
| BstX2I | RGATCY | 5 cut(s) | 2246, 2333, 2755, 2947, 4171 |
| BstXI | CCANNNNNNTGG | 3 cut(s) | 482, 1502, 3480 |
| BstYI | RGATCY | 5 cut(s) | 2246, 2333, 2755, 2947, 4171 |
| BstZ17I | GTATAC | 1 cut(s) | 2942 |
| Bsu15I | ATCGAT | 1 cut(s) | 2470 |
| Bsu36I | CCTNAGG | 1 cut(s) | 2421 |
| BsuI | GTATCC | 2 cut(s) | 3802, 3888 |
| BsuRI | GGCC | 5 cut(s) | 578, 1209, 2742, 3757, 4008 |
| BsuTUI | ATCGAT | 1 cut(s) | 2470 |
| BtgI | CCRYGG | 1 cut(s) | 495 |
| BtrI | CACGTC | 3 cut(s) | 1223, 1241, 2707 |
| BtsCI | GGATG | 8 cut(s) | 33, 1599, 1800, 1982, 3070, 3343, 3698, 3978 |
| BtsI | GCAGTG | 1 cut(s) | 11 |
| BtsIMutI | CAGTG | 5 cut(s) | 11, 537, 624, 1545, 3108 |
| BveI | ACCTGC | 1 cut(s) | 2854 |
| Cac8I | GCNNGC | 9 cut(s) | 777, 1076, 1435, 1489, 2744, 2748, 2811, 3950, 4074 |
| CciI | TCATGA | 2 cut(s) | 3535, 3615 |
| CfoI | GCGC | 4 cut(s) | 1318, 1487, 3472, 4072 |
| Cfr10I | RCCGGY | 2 cut(s) | 1481, 4246 |
| Cfr13I | GGNCC | 5 cut(s) | 577, 994, 2072, 2741, 3860 |
| ClaI | ATCGAT | 1 cut(s) | 2470 |
| CseI | GACGC | 2 cut(s) | 1147, 1254 |
| CsiI | ACCWGGT | 1 cut(s) | 2530 |
| DinI | GGCGCC | 1 cut(s) | 1486 |
| DraI | TTTAAA | 1 cut(s) | 469 |
| DraIII | CACNNNGTG | 1 cut(s) | 3528 |
| DriI | GACNNNNNGTC | 1 cut(s) | 3866 |
| EaeI | YGGCCR | 1 cut(s) | 1207 |
| Eam1104I | CTCTTC | 6 cut(s) | 1023, 1086, 1100, 1404, 2123, 2778 |
| Eam1105I | GACNNNNNGTC | 1 cut(s) | 3866 |
| EarI | CTCTTC | 6 cut(s) | 1023, 1086, 1100, 1404, 2123, 2778 |
| EciI | GGCGGA | 3 cut(s) | 757, 2372, 3337 |
| Ecl136II | GAGCTC | 3 cut(s) | 1358, 1528, 2050 |
| Eco130I | CCWWGG | 3 cut(s) | 495, 1770, 3848 |
| Eco24I | GRGCYC | 5 cut(s) | 1076, 1360, 1530, 2035, 2052 |
| Eco31I | GGTCTC | 1 cut(s) | 757 |
| Eco47I | GGWCC | 3 cut(s) | 994, 2072, 3860 |
| Eco47III | AGCGCT | 2 cut(s) | 1317, 4071 |
| Eco53kI | GAGCTC | 3 cut(s) | 1358, 1528, 2050 |
| Eco57I | CTGAAG | 6 cut(s) | 2180, 3455, 3461, 3623, 3798, 4197 |
| Eco81I | CCTNAGG | 1 cut(s) | 2421 |
| Eco88I | CYCGRG | 1 cut(s) | 3795 |
| Eco91I | GGTNACC | 1 cut(s) | 1625 |
| EcoICRI | GAGCTC | 3 cut(s) | 1358, 1528, 2050 |
| EcoO109I | RGGNCCY | 1 cut(s) | 577 |
| EcoO65I | GGTNACC | 1 cut(s) | 1625 |
| EcoRI | GAATTC | 4 cut(s) | 163, 2264, 2307, 4253 |
| EcoRII | CCWGG | 2 cut(s) | 2144, 2530 |
| EcoT14I | CCWWGG | 3 cut(s) | 495, 1770, 3848 |
| EcoT38I | GRGCYC | 5 cut(s) | 1076, 1360, 1530, 2035, 2052 |
| EgeI | GGCGCC | 1 cut(s) | 1486 |
| EheI | GGCGCC | 1 cut(s) | 1486 |
| ErhI | CCWWGG | 3 cut(s) | 495, 1770, 3848 |
| Esp3I | CGTCTC | 2 cut(s) | 1557, 2697 |
| FalI | AAGNNNNNCTT | 2 cut(s) | 3335, 3367 |
| FaqI | GGGAC | 5 cut(s) | 105, 637, 2812, 3814, 3919 |
| FauI | CCCGC | 1 cut(s) | 2751 |
| FauNDI | CATATG | 1 cut(s) | 1087 |
| FbaI | TGATCA | 2 cut(s) | 1960, 2694 |
| FblI | GTMKAC | 7 cut(s) | 1647, 2021, 2314, 2457, 2941, 3018, 3381 |
| Fnu4HI | GCNGC | 5 cut(s) | 516, 1127, 3306, 4112, 4208 |
| FokI | GGATG | 8 cut(s) | 20, 1586, 1807, 1989, 3077, 3350, 3705, 3985 |
| FriOI | GRGCYC | 5 cut(s) | 1076, 1360, 1530, 2035, 2052 |
| Fsp4HI | GCNGC | 5 cut(s) | 516, 1127, 3306, 4112, 4208 |
| FspBI | CTAG | 5 cut(s) | 1430, 3206, 3849, 3969, 4010 |
| GlaI | GCGC | 4 cut(s) | 1317, 1486, 3471, 4071 |
| GluI | GCNGC | 5 cut(s) | 516, 1127, 3306, 4112, 4208 |
| HaeII | RGCGCY | 4 cut(s) | 1319, 1488, 3473, 4073 |
| HaeIII | GGCC | 5 cut(s) | 578, 1209, 2742, 3757, 4008 |
| HapII | CCGG | 3 cut(s) | 1482, 3234, 4247 |
| HgaI | GACGC | 2 cut(s) | 1147, 1254 |
| HhaI | GCGC | 4 cut(s) | 1318, 1487, 3472, 4072 |
| Hin1I | GRCGYC | 1 cut(s) | 1485 |
| Hin6I | GCGC | 4 cut(s) | 1316, 1485, 3470, 4070 |
| HinP1I | GCGC | 4 cut(s) | 1316, 1485, 3470, 4070 |
| HincII | GTYRAC | 4 cut(s) | 1691, 2022, 2315, 3019 |
| HindII | GTYRAC | 4 cut(s) | 1691, 2022, 2315, 3019 |
| HindIII | AAGCTT | 4 cut(s) | 788, 1168, 2005, 4160 |
| HpaII | CCGG | 3 cut(s) | 1482, 3234, 4247 |
| HphI | GGTGA | 9 cut(s) | 81, 863, 956, 1619, 1942, 2704, 2844, 2871, 3514 |
| Hpy99I | CGWCG | 5 cut(s) | 2210, 2316, 2609, 2720, 3665 |
| HpyCH4III | ACNGT | 8 cut(s) | 944, 1944, 2326, 2692, 3112, 3910, 4021, 4308 |
| Hsp92I | GRCGYC | 1 cut(s) | 1485 |
| HspAI | GCGC | 4 cut(s) | 1316, 1485, 3470, 4070 |
| KasI | GGCGCC | 1 cut(s) | 1484 |
| Ksp22I | TGATCA | 2 cut(s) | 1960, 2694 |
| LmnI | GCTCC | 6 cut(s) | 587, 809, 1363, 2183, 2806, 2904 |
| Lsp1109I | GCAGC | 4 cut(s) | 527, 1138, 3317, 4098 |
| LweI | GCATC | 6 cut(s) | 1879, 1894, 1956, 2894, 3501, 4194 |
| MabI | ACCWGGT | 1 cut(s) | 2530 |
| MaeI | CTAG | 5 cut(s) | 1430, 3206, 3849, 3969, 4010 |
| MaeIII | GTNAC | 7 cut(s) | 374, 419, 1018, 1595, 1625, 1844, 2707 |
| MflI | RGATCY | 5 cut(s) | 2246, 2333, 2755, 2947, 4171 |
| Mly113I | GGCGCC | 1 cut(s) | 1485 |
| MlyI | GAGTC | 5 cut(s) | 2027, 2494, 2636, 3150, 3372 |
| MmeI | TCCRAC | 4 cut(s) | 972, 1232, 2501, 3957 |
| MroXI | GAANNNNTTC | 2 cut(s) | 4257, 4276 |
| MslI | CAYNNNNRTG | 7 cut(s) | 1016, 1239, 1500, 2061, 2063, 2574, 3540 |
| MspA1I | CMGCKG | 2 cut(s) | 415, 4141 |
| MspCI | CTTAAG | 2 cut(s) | 1835, 4163 |
| MspI | CCGG | 3 cut(s) | 1482, 3234, 4247 |
| MspR9I | CCNGG | 2 cut(s) | 2146, 2532 |
| Mva1269I | GAATGC | 2 cut(s) | 300, 2186 |
| MvaI | CCWGG | 2 cut(s) | 2146, 2532 |
| MvnI | CGCG | 1 cut(s) | 1218 |
| NarI | GGCGCC | 1 cut(s) | 1485 |
| NcoI | CCATGG | 1 cut(s) | 495 |
| NdeI | CATATG | 1 cut(s) | 1087 |
| NlaIV | GGNNCC | 5 cut(s) | 811, 996, 1486, 2906, 4173 |
| NmeAIII | GCCGAG | 1 cut(s) | 1235 |
| NmuCI | GTSAC | 3 cut(s) | 1018, 1625, 2707 |
| NspI | RCATGY | 7 cut(s) | 1145, 1437, 1501, 2451, 2579, 2750, 3545 |
| NspV | TTCGAA | 1 cut(s) | 858 |
| OliI | CACNNNNGTG | 2 cut(s) | 1500, 2063 |
| PaeI | GCATGC | 2 cut(s) | 1437, 2750 |
| PagI | TCATGA | 2 cut(s) | 3535, 3615 |
| PaqCI | CACCTGC | 1 cut(s) | 2854 |
| PciI | ACATGT | 2 cut(s) | 1497, 2575 |
| PcsI | WCGNNNNNNNCGW | 4 cut(s) | 2712, 3081, 3183, 3669 |
| PctI | GAATGC | 2 cut(s) | 300, 2186 |
| PdmI | GAANNNNTTC | 2 cut(s) | 4257, 4276 |
| PflMI | CCANNNNNTGG | 1 cut(s) | 2681 |
| PkrI | GCNGC | 5 cut(s) | 517, 1128, 3307, 4113, 4209 |
| PleI | GAGTC | 5 cut(s) | 2026, 2494, 2636, 3149, 3371 |
| PluTI | GGCGCC | 1 cut(s) | 1488 |
| PpsI | GAGTC | 5 cut(s) | 2026, 2494, 2636, 3149, 3371 |
| Ppu21I | YACGTR | 1 cut(s) | 1654 |
| PscI | ACATGT | 2 cut(s) | 1497, 2575 |
| PshBI | ATTAAT | 2 cut(s) | 1634, 1763 |
| Psp124BI | GAGCTC | 3 cut(s) | 1360, 1530, 2052 |
| Psp1406I | AACGTT | 1 cut(s) | 1551 |
| Psp6I | CCWGG | 2 cut(s) | 2144, 2530 |
| PspEI | GGTNACC | 1 cut(s) | 1625 |
| PspGI | CCWGG | 2 cut(s) | 2144, 2530 |
| PspN4I | GGNNCC | 5 cut(s) | 811, 996, 1486, 2906, 4173 |
| PspPI | GGNCC | 5 cut(s) | 577, 994, 2072, 2741, 3860 |
| PsuI | RGATCY | 5 cut(s) | 2246, 2333, 2755, 2947, 4171 |
| PvuII | CAGCTG | 1 cut(s) | 4141 |
| RseI | CAYNNNNRTG | 7 cut(s) | 1016, 1239, 1500, 2061, 2063, 2574, 3540 |
| SacI | GAGCTC | 3 cut(s) | 1360, 1530, 2052 |
| SalI | GTCGAC | 3 cut(s) | 2020, 2313, 3017 |
| SatI | GCNGC | 5 cut(s) | 516, 1127, 3306, 4112, 4208 |
| Sau96I | GGNCC | 5 cut(s) | 577, 994, 2072, 2741, 3860 |
| ScaI | AGTACT | 2 cut(s) | 3503, 3811 |
| SchI | GAGTC | 5 cut(s) | 2027, 2494, 2636, 3150, 3372 |
| ScrFI | CCNGG | 2 cut(s) | 2146, 2532 |
| SexAI | ACCWGGT | 1 cut(s) | 2530 |
| SfaNI | GCATC | 6 cut(s) | 1879, 1894, 1956, 2894, 3501, 4194 |
| SfcI | CTRYAG | 1 cut(s) | 3220 |
| SfoI | GGCGCC | 1 cut(s) | 1486 |
| SfuI | TTCGAA | 1 cut(s) | 858 |
| SgrAI | CRCCGGYG | 1 cut(s) | 1481 |
| SinI | GGWCC | 3 cut(s) | 994, 2072, 3860 |
| SmiMI | CAYNNNNRTG | 7 cut(s) | 1016, 1239, 1500, 2061, 2063, 2574, 3540 |
| SmlI | CTYRAG | 7 cut(s) | 754, 904, 1133, 1325, 1835, 2045, 4163 |
| SmoI | CTYRAG | 7 cut(s) | 754, 904, 1133, 1325, 1835, 2045, 4163 |
| SpeI | ACTAGT | 1 cut(s) | 3205 |
| SphI | GCATGC | 2 cut(s) | 1437, 2750 |
| SspDI | GGCGCC | 1 cut(s) | 1484 |
| SspI | AATATT | 1 cut(s) | 386 |
| SspMI | CTAG | 5 cut(s) | 1430, 3206, 3849, 3969, 4010 |
| SstI | GAGCTC | 3 cut(s) | 1360, 1530, 2052 |
| StyD4I | CCNGG | 2 cut(s) | 2144, 2530 |
| StyI | CCWWGG | 3 cut(s) | 495, 1770, 3848 |
| TaaI | ACNGT | 8 cut(s) | 944, 1944, 2326, 2692, 3112, 3910, 4021, 4308 |
| TaqII | GACCGA | 1 cut(s) | 3877 |
| TatI | WGTACW | 6 cut(s) | 2572, 3034, 3153, 3501, 3809, 4143 |
| TauI | GCSGC | 1 cut(s) | 4210 |
| TscAI | CASTG | 5 cut(s) | 18, 537, 631, 1545, 3115 |
| TseFI | GTSAC | 3 cut(s) | 1018, 1625, 2707 |
| TseI | GCWGC | 4 cut(s) | 515, 1126, 3305, 4111 |
| Tsp45I | GTSAC | 3 cut(s) | 1018, 1625, 2707 |
| TspGWI | ACGGA | 1 cut(s) | 3192 |
| TspRI | CASTG | 5 cut(s) | 18, 537, 631, 1545, 3115 |
| Van91I | CCANNNNNTGG | 1 cut(s) | 2681 |
| Vha464I | CTTAAG | 2 cut(s) | 1835, 4163 |
| VpaK11BI | GGWCC | 3 cut(s) | 994, 2072, 3860 |
| VspI | ATTAAT | 2 cut(s) | 1634, 1763 |
| XceI | RCATGY | 7 cut(s) | 1145, 1437, 1501, 2451, 2579, 2750, 3545 |
| XmaJI | CCTAGG | 1 cut(s) | 3848 |
| XmiI | GTMKAC | 7 cut(s) | 1647, 2021, 2314, 2457, 2941, 3018, 3381 |
| XmnI | GAANNNNTTC | 2 cut(s) | 4257, 4276 |
| XspI | CTAG | 5 cut(s) | 1430, 3206, 3849, 3969, 4010 |
| ZrmI | AGTACT | 2 cut(s) | 3503, 3811 |