gag-polypeptide of LTR copia-type
| Domain Name | Pfam ID | Position | E-value | Description |
|---|---|---|---|---|
| Retrotran_gag_3 | PF14244 | 29 - 76 | 5.2e-16 | gag-polypeptide of LTR copia-type |
| Retrotran_gag_2 | PF14223 | 55 - 163 | 6.1e-08 | gag-polypeptide of LTR copia-type |
| Pol_BBD | PF22936 | 381 - 453 | 1.4e-12 | Pol polyprotein, beta-barrel domain |
| gag_pre-integrs | PF13976 | 486 - 545 | 1.6e-07 | GAG-pre-integrase domain |
| rve | PF00665 | 562 - 656 | 9.9e-11 | Integrase core domain |
| SH3_retrovirus | PF25597 | 730 - 791 | 3.4e-24 | Retroviral polymerase SH3-like domain |
| RVT_2 | PF07727 | 900 - 1111 | 1.1e-67 | Reverse transcriptase (RNA-dependent DNA polymerase) |
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| Enzyme | Recognition Site | Cut Count | Positions (bp) |
|---|---|---|---|
| AanI | TTATAA | 1 cut(s) | 1716 |
| AarI | CACCTGC | 1 cut(s) | 2542 |
| Acc16I | TGCGCA | 1 cut(s) | 234 |
| Acc36I | ACCTGC | 3 cut(s) | 226, 2052, 2542 |
| Acc65I | GGTACC | 1 cut(s) | 2265 |
| AccB1I | GGYRCC | 5 cut(s) | 104, 1157, 1527, 1542, 2265 |
| AccB7I | CCANNNNNTGG | 2 cut(s) | 2991, 3472 |
| AccII | CGCG | 3 cut(s) | 344, 346, 743 |
| AccIII | TCCGGA | 1 cut(s) | 1003 |
| AcoI | YGGCCR | 1 cut(s) | 1267 |
| AcsI | RAATTY | 3 cut(s) | 420, 1333, 2228 |
| AcuI | CTGAAG | 1 cut(s) | 1010 |
| AcyI | GRCGYC | 1 cut(s) | 105 |
| AdeI | CACNNNGTG | 1 cut(s) | 1776 |
| AfaI | GTAC | 7 cut(s) | 859, 1317, 2101, 2267, 2897, 3728, 3940 |
| AflIII | ACRYGT | 5 cut(s) | 1207, 1592, 2176, 2612, 3746 |
| AjiI | CACGTC | 4 cut(s) | 519, 1197, 2615, 2653 |
| AjnI | CCWGG | 7 cut(s) | 100, 951, 1781, 2714, 2911, 3538, 3674 |
| AleI | CACNNNNGTG | 1 cut(s) | 152 |
| AluBI | AGCT | 6 cut(s) | 662, 1030, 1515, 1820, 2950, 3443 |
| AluI | AGCT | 6 cut(s) | 662, 1030, 1515, 1820, 2950, 3443 |
| Alw21I | GWGCWC | 8 cut(s) | 847, 1517, 1584, 1781, 2026, 2245, 2808, 3538 |
| Alw26I | GTCTC | 5 cut(s) | 554, 770, 1918, 2651, 2927 |
| Alw44I | GTGCAC | 4 cut(s) | 1580, 1777, 2241, 3534 |
| AlwNI | CAGNNNCTG | 1 cut(s) | 917 |
| Ama87I | CYCGRG | 2 cut(s) | 1898, 2328 |
| Aor13HI | TCCGGA | 1 cut(s) | 1003 |
| AoxI | GGCC | 5 cut(s) | 171, 935, 1267, 2082, 3431 |
| ApaLI | GTGCAC | 4 cut(s) | 1580, 1777, 2241, 3534 |
| ApoI | RAATTY | 3 cut(s) | 420, 1333, 2228 |
| AseI | ATTAAT | 1 cut(s) | 1688 |
| Asp700I | GAANNNNTTC | 3 cut(s) | 1856, 3161, 3918 |
| Asp718I | GGTACC | 1 cut(s) | 2265 |
| AspLEI | GCGC | 5 cut(s) | 107, 235, 346, 670, 1739 |
| AspS9I | GGNCC | 2 cut(s) | 1411, 1895 |
| AsuC2I | CCSGG | 3 cut(s) | 2329, 2330, 3860 |
| AsuII | TTCGAA | 3 cut(s) | 1882, 2346, 3854 |
| AvaI | CYCGRG | 2 cut(s) | 1898, 2328 |
| AvaII | GGWCC | 2 cut(s) | 1411, 1895 |
| AxyI | CCTNAGG | 1 cut(s) | 732 |
| BaeGI | GKGCMC | 5 cut(s) | 1545, 1584, 1781, 2245, 3538 |
| BamHI | GGATCC | 4 cut(s) | 637, 1487, 1935, 3569 |
| BanI | GGYRCC | 5 cut(s) | 104, 1157, 1527, 1542, 2265 |
| BanII | GRGCYC | 2 cut(s) | 1517, 3336 |
| BauI | CACGAG | 4 cut(s) | 128, 2019, 2238, 2937 |
| BbsI | GAAGAC | 3 cut(s) | 141, 1095, 1554 |
| Bbv12I | GWGCWC | 8 cut(s) | 847, 1517, 1584, 1781, 2026, 2245, 2808, 3538 |
| BccI | CCATC | 9 cut(s) | 78, 116, 172, 200, 779, 1555, 2440, 2548, 3568 |
| BceAI | ACGGC | 2 cut(s) | 3957, 3973 |
| BciT130I | CCWGG | 7 cut(s) | 102, 953, 1783, 2716, 2913, 3540, 3676 |
| BcnI | CCSGG | 3 cut(s) | 2329, 2330, 3860 |
| BcoDI | GTCTC | 5 cut(s) | 554, 770, 1918, 2651, 2927 |
| BfaI | CTAG | 4 cut(s) | 2849, 3483, 3609, 3711 |
| BfmI | CTRYAG | 2 cut(s) | 2734, 3388 |
| BfoI | RGCGCY | 1 cut(s) | 108 |
| BfuAI | ACCTGC | 3 cut(s) | 226, 2052, 2542 |
| BlpI | GCTNAGC | 1 cut(s) | 4019 |
| Bme18I | GGWCC | 2 cut(s) | 1411, 1895 |
| BmeT110I | CYCGRG | 2 cut(s) | 1898, 2328 |
| BmgBI | CACGTC | 4 cut(s) | 519, 1197, 2615, 2653 |
| BmgT120I | GGNCC | 2 cut(s) | 1411, 1895 |
| BmrI | ACTGGG | 1 cut(s) | 3613 |
| BmsI | GCATC | 9 cut(s) | 220, 487, 788, 2056, 2210, 3255, 3280, 3367, 3602 |
| BmuI | ACTGGG | 1 cut(s) | 3613 |
| BoxI | GACNNNNGTC | 1 cut(s) | 930 |
| BpiI | GAAGAC | 3 cut(s) | 141, 1095, 1554 |
| BplI | GAGNNNNNCTC | 2 cut(s) | 1443, 1475 |
| BpmI | CTGGAG | 1 cut(s) | 2968 |
| Bpu1102I | GCTNAGC | 1 cut(s) | 4019 |
| Bpu14I | TTCGAA | 3 cut(s) | 1882, 2346, 3854 |
| BpuEI | CTTGAG | 4 cut(s) | 836, 1675, 3002, 4075 |
| BpuMI | CCSGG | 3 cut(s) | 2329, 2330, 3860 |
| Bsa29I | ATCGAT | 1 cut(s) | 3632 |
| BsaAI | YACGTR | 1 cut(s) | 2177 |
| BsaBI | GATNNNNATC | 1 cut(s) | 1602 |
| BsaHI | GRCGYC | 1 cut(s) | 105 |
| BsaI | GGTCTC | 1 cut(s) | 2651 |
| BsaWI | WCCGGW | 2 cut(s) | 1003, 2776 |
| Bse1I | ACTGG | 4 cut(s) | 1950, 3466, 3608, 3809 |
| Bse21I | CCTNAGG | 1 cut(s) | 732 |
| Bse3DI | GCAATG | 6 cut(s) | 260, 523, 641, 3087, 3846, 4013 |
| Bse8I | GATNNNNATC | 1 cut(s) | 1602 |
| BseAI | TCCGGA | 1 cut(s) | 1003 |
| BseBI | CCWGG | 7 cut(s) | 102, 953, 1783, 2716, 2913, 3540, 3676 |
| BseCI | ATCGAT | 1 cut(s) | 3632 |
| BseGI | GGATG | 7 cut(s) | 70, 108, 493, 2071, 2338, 2540, 3383 |
| BseJI | GATNNNNATC | 1 cut(s) | 1602 |
| BseMI | GCAATG | 6 cut(s) | 260, 523, 641, 3087, 3846, 4013 |
| BseMII | CTCAG | 7 cut(s) | 330, 578, 723, 765, 1176, 1746, 4033 |
| BseNI | ACTGG | 4 cut(s) | 1950, 3466, 3608, 3809 |
| BseRI | GAGGAG | 3 cut(s) | 2442, 2536, 2620 |
| BseSI | GKGCMC | 5 cut(s) | 1545, 1584, 1781, 2245, 3538 |
| BsgI | GTGCAG | 3 cut(s) | 2520, 2571, 3735 |
| Bsh1236I | CGCG | 3 cut(s) | 344, 346, 743 |
| Bsh1285I | CGRYCG | 1 cut(s) | 2923 |
| BshFI | GGCC | 5 cut(s) | 173, 937, 1269, 2084, 3433 |
| BshNI | GGYRCC | 5 cut(s) | 104, 1157, 1527, 1542, 2265 |
| BshVI | ATCGAT | 1 cut(s) | 3632 |
| BsiEI | CGRYCG | 1 cut(s) | 2923 |
| BsiHKAI | GWGCWC | 8 cut(s) | 847, 1517, 1584, 1781, 2026, 2245, 2808, 3538 |
| BsiHKCI | CYCGRG | 2 cut(s) | 1898, 2328 |
| BsiSI | CCGG | 5 cut(s) | 1004, 2329, 2777, 3434, 3860 |
| BsiWI | CGTACG | 1 cut(s) | 3938 |
| BslFI | GGGAC | 9 cut(s) | 891, 1450, 1470, 1605, 1881, 2311, 2656, 3210, 3797 |
| BsmAI | GTCTC | 5 cut(s) | 554, 770, 1918, 2651, 2927 |
| BsmFI | GGGAC | 9 cut(s) | 891, 1450, 1470, 1605, 1881, 2311, 2656, 3210, 3797 |
| BsnI | GGCC | 5 cut(s) | 173, 937, 1269, 2084, 3433 |
| Bso31I | GGTCTC | 1 cut(s) | 2651 |
| BsoBI | CYCGRG | 2 cut(s) | 1898, 2328 |
| Bsp119I | TTCGAA | 3 cut(s) | 1882, 2346, 3854 |
| Bsp13I | TCCGGA | 1 cut(s) | 1003 |
| Bsp1407I | TGTACA | 2 cut(s) | 857, 2895 |
| Bsp1720I | GCTNAGC | 1 cut(s) | 4019 |
| Bsp19I | CCATGG | 3 cut(s) | 168, 2272, 3735 |
| BspANI | GGCC | 5 cut(s) | 173, 937, 1269, 2084, 3433 |
| BspCNI | CTCAG | 7 cut(s) | 329, 577, 724, 766, 1177, 1745, 4032 |
| BspDI | ATCGAT | 1 cut(s) | 3632 |
| BspEI | TCCGGA | 1 cut(s) | 1003 |
| BspFNI | CGCG | 3 cut(s) | 344, 346, 743 |
| BspHI | TCATGA | 3 cut(s) | 682, 1084, 3868 |
| BspMI | ACCTGC | 3 cut(s) | 226, 2052, 2542 |
| BspQI | GCTCTTC | 2 cut(s) | 1522, 2503 |
| BspT104I | TTCGAA | 3 cut(s) | 1882, 2346, 3854 |
| BspT107I | GGYRCC | 5 cut(s) | 104, 1157, 1527, 1542, 2265 |
| BspTNI | GGTCTC | 1 cut(s) | 2651 |
| BsrDI | GCAATG | 6 cut(s) | 260, 523, 641, 3087, 3846, 4013 |
| BsrGI | TGTACA | 2 cut(s) | 857, 2895 |
| BsrI | ACTGG | 4 cut(s) | 1950, 3466, 3608, 3809 |
| BssNI | GRCGYC | 1 cut(s) | 105 |
| BssSI | CACGAG | 4 cut(s) | 128, 2019, 2238, 2937 |
| BssT1I | CCWWGG | 8 cut(s) | 168, 942, 1478, 1537, 1623, 2272, 2727, 3735 |
| Bst2BI | CACGAG | 4 cut(s) | 128, 2019, 2238, 2937 |
| Bst2UI | CCWGG | 7 cut(s) | 102, 953, 1783, 2716, 2913, 3540, 3676 |
| Bst6I | CTCTTC | 4 cut(s) | 1522, 2118, 2462, 2503 |
| BstACI | GRCGYC | 1 cut(s) | 105 |
| BstAUI | TGTACA | 2 cut(s) | 857, 2895 |
| BstBAI | YACGTR | 1 cut(s) | 2177 |
| BstBI | TTCGAA | 3 cut(s) | 1882, 2346, 3854 |
| BstC8I | GCNNGC | 3 cut(s) | 1016, 2948, 2979 |
| BstDSI | CCRYGG | 3 cut(s) | 168, 2272, 3735 |
| BstEII | GGTNACC | 1 cut(s) | 2285 |
| BstENI | CCTNNNNNAGG | 3 cut(s) | 1324, 2490, 3391 |
| BstF5I | GGATG | 7 cut(s) | 70, 108, 493, 2071, 2338, 2540, 3383 |
| BstFNI | CGCG | 3 cut(s) | 344, 346, 743 |
| BstH2I | RGCGCY | 1 cut(s) | 108 |
| BstHHI | GCGC | 5 cut(s) | 107, 235, 346, 670, 1739 |
| BstMAI | GTCTC | 5 cut(s) | 554, 770, 1918, 2651, 2927 |
| BstMCI | CGRYCG | 1 cut(s) | 2923 |
| BstMWI | GCNNNNNNNGC | 7 cut(s) | 355, 364, 807, 2780, 2833, 3020, 3605 |
| BstNI | CCWGG | 7 cut(s) | 102, 953, 1783, 2716, 2913, 3540, 3676 |
| BstNSI | RCATGY | 3 cut(s) | 2170, 2902, 3750 |
| BstPAI | GACNNNNGTC | 1 cut(s) | 930 |
| BstPI | GGTNACC | 1 cut(s) | 2285 |
| BstSFI | CTRYAG | 2 cut(s) | 2734, 3388 |
| BstSLI | GKGCMC | 5 cut(s) | 1545, 1584, 1781, 2245, 3538 |
| BstUI | CGCG | 3 cut(s) | 344, 346, 743 |
| BstV2I | GAAGAC | 3 cut(s) | 141, 1095, 1554 |
| BstX2I | RGATCY | 4 cut(s) | 637, 1487, 1935, 3569 |
| BstXI | CCANNNNNNTGG | 4 cut(s) | 169, 1066, 1538, 3991 |
| BstYI | RGATCY | 4 cut(s) | 637, 1487, 1935, 3569 |
| Bsu15I | ATCGAT | 1 cut(s) | 3632 |
| Bsu36I | CCTNAGG | 1 cut(s) | 732 |
| BsuRI | GGCC | 5 cut(s) | 173, 937, 1269, 2084, 3433 |
| BsuTUI | ATCGAT | 1 cut(s) | 3632 |
| BtgI | CCRYGG | 3 cut(s) | 168, 2272, 3735 |
| BtgZI | GCGATG | 1 cut(s) | 811 |
| BtrI | CACGTC | 4 cut(s) | 519, 1197, 2615, 2653 |
| BtsCI | GGATG | 7 cut(s) | 70, 108, 493, 2071, 2338, 2540, 3383 |
| BtsI | GCAGTG | 2 cut(s) | 331, 2583 |
| BtsIMutI | CAGTG | 7 cut(s) | 331, 756, 1159, 2583, 2793, 2837, 3696 |
| BveI | ACCTGC | 3 cut(s) | 226, 2052, 2542 |
| Cac8I | GCNNGC | 3 cut(s) | 1016, 2948, 2979 |
| CaiI | CAGNNNCTG | 1 cut(s) | 917 |
| CciI | TCATGA | 3 cut(s) | 682, 1084, 3868 |
| CfoI | GCGC | 5 cut(s) | 107, 235, 346, 670, 1739 |
| Cfr13I | GGNCC | 2 cut(s) | 1411, 1895 |
| Cfr9I | CCCGGG | 1 cut(s) | 2328 |
| ClaI | ATCGAT | 1 cut(s) | 3632 |
| CseI | GACGC | 3 cut(s) | 350, 2816, 3605 |
| CsiI | ACCWGGT | 1 cut(s) | 951 |
| Csp6I | GTAC | 7 cut(s) | 858, 1316, 2100, 2266, 2896, 3727, 3939 |
| CspCI | CAANNNNNGTGG | 2 cut(s) | 3988, 4023 |
| CviQI | GTAC | 7 cut(s) | 858, 1316, 2100, 2266, 2896, 3727, 3939 |
| DinI | GGCGCC | 1 cut(s) | 106 |
| DraI | TTTAAA | 1 cut(s) | 2973 |
| DraIII | CACNNNGTG | 1 cut(s) | 1776 |
| EaeI | YGGCCR | 1 cut(s) | 1267 |
| Eam1104I | CTCTTC | 4 cut(s) | 1522, 2118, 2462, 2503 |
| EarI | CTCTTC | 4 cut(s) | 1522, 2118, 2462, 2503 |
| EciI | GGCGGA | 1 cut(s) | 2397 |
| Ecl136II | GAGCTC | 1 cut(s) | 1515 |
| Eco130I | CCWWGG | 8 cut(s) | 168, 942, 1478, 1537, 1623, 2272, 2727, 3735 |
| Eco24I | GRGCYC | 2 cut(s) | 1517, 3336 |
| Eco31I | GGTCTC | 1 cut(s) | 2651 |
| Eco32I | GATATC | 3 cut(s) | 1341, 3672, 4078 |
| Eco47I | GGWCC | 2 cut(s) | 1411, 1895 |
| Eco53kI | GAGCTC | 1 cut(s) | 1515 |
| Eco57I | CTGAAG | 1 cut(s) | 1010 |
| Eco81I | CCTNAGG | 1 cut(s) | 732 |
| Eco88I | CYCGRG | 2 cut(s) | 1898, 2328 |
| Eco91I | GGTNACC | 1 cut(s) | 2285 |
| EcoICRI | GAGCTC | 1 cut(s) | 1515 |
| EcoNI | CCTNNNNNAGG | 3 cut(s) | 1324, 2490, 3391 |
| EcoO109I | RGGNCCY | 1 cut(s) | 1411 |
| EcoO65I | GGTNACC | 1 cut(s) | 2285 |
| EcoRII | CCWGG | 7 cut(s) | 100, 951, 1781, 2714, 2911, 3538, 3674 |
| EcoRV | GATATC | 3 cut(s) | 1341, 3672, 4078 |
| EcoT14I | CCWWGG | 8 cut(s) | 168, 942, 1478, 1537, 1623, 2272, 2727, 3735 |
| EcoT22I | ATGCAT | 2 cut(s) | 2172, 3274 |
| EcoT38I | GRGCYC | 2 cut(s) | 1517, 3336 |
| EgeI | GGCGCC | 1 cut(s) | 106 |
| EheI | GGCGCC | 1 cut(s) | 106 |
| ErhI | CCWWGG | 8 cut(s) | 168, 942, 1478, 1537, 1623, 2272, 2727, 3735 |
| FalI | AAGNNNNNCTT | 8 cut(s) | 922, 954, 1809, 1841, 3351, 3383, 3557, 3589 |
| FaqI | GGGAC | 9 cut(s) | 891, 1450, 1470, 1605, 1881, 2311, 2656, 3210, 3797 |
| FauI | CCCGC | 1 cut(s) | 2575 |
| FauNDI | CATATG | 3 cut(s) | 553, 604, 3456 |
| FokI | GGATG | 7 cut(s) | 57, 95, 500, 2078, 2345, 2527, 3370 |
| FriOI | GRGCYC | 2 cut(s) | 1517, 3336 |
| FspBI | CTAG | 4 cut(s) | 2849, 3483, 3609, 3711 |
| FspI | TGCGCA | 1 cut(s) | 234 |
| GlaI | GCGC | 5 cut(s) | 106, 234, 345, 669, 1738 |
| GsuI | CTGGAG | 1 cut(s) | 2968 |
| HaeII | RGCGCY | 1 cut(s) | 108 |
| HaeIII | GGCC | 5 cut(s) | 173, 937, 1269, 2084, 3433 |
| HapII | CCGG | 5 cut(s) | 1004, 2329, 2777, 3434, 3860 |
| HgaI | GACGC | 3 cut(s) | 350, 2816, 3605 |
| HhaI | GCGC | 5 cut(s) | 107, 235, 346, 670, 1739 |
| Hin1I | GRCGYC | 1 cut(s) | 105 |
| Hin6I | GCGC | 5 cut(s) | 105, 233, 344, 668, 1737 |
| HinP1I | GCGC | 5 cut(s) | 105, 233, 344, 668, 1737 |
| HincII | GTYRAC | 7 cut(s) | 24, 655, 1960, 2755, 2790, 2857, 3260 |
| HindII | GTYRAC | 7 cut(s) | 24, 655, 1960, 2755, 2790, 2857, 3260 |
| HindIII | AAGCTT | 1 cut(s) | 660 |
| HpaI | GTTAAC | 2 cut(s) | 655, 2790 |
| HpaII | CCGG | 5 cut(s) | 1004, 2329, 2777, 3434, 3860 |
| Hpy188I | TCNGA | 5 cut(s) | 94, 567, 1810, 3049, 3068 |
| Hpy99I | CGWCG | 4 cut(s) | 520, 2250, 2607, 2657 |
| HpyCH4IV | ACGT | 9 cut(s) | 493, 518, 1196, 1207, 1417, 1592, 2176, 2614, 2652 |
| HpyF10VI | GCNNNNNNNGC | 7 cut(s) | 355, 364, 807, 2780, 2833, 3020, 3605 |
| HpySE526I | ACGT | 9 cut(s) | 493, 518, 1196, 1207, 1417, 1592, 2176, 2614, 2652 |
| Hsp92I | GRCGYC | 1 cut(s) | 105 |
| HspAI | GCGC | 5 cut(s) | 105, 233, 344, 668, 1737 |
| KasI | GGCGCC | 1 cut(s) | 104 |
| Kpn2I | TCCGGA | 1 cut(s) | 1003 |
| KpnI | GGTACC | 1 cut(s) | 2269 |
| KspAI | GTTAAC | 2 cut(s) | 655, 2790 |
| LguI | GCTCTTC | 2 cut(s) | 1522, 2503 |
| LmnI | GCTCC | 5 cut(s) | 806, 2686, 2779, 2811, 3331 |
| LweI | GCATC | 9 cut(s) | 220, 487, 788, 2056, 2210, 3255, 3280, 3367, 3602 |
| MabI | ACCWGGT | 1 cut(s) | 951 |
| MaeI | CTAG | 4 cut(s) | 2849, 3483, 3609, 3711 |
| MaeII | ACGT | 9 cut(s) | 493, 518, 1196, 1207, 1417, 1592, 2176, 2614, 2652 |
| MflI | RGATCY | 4 cut(s) | 637, 1487, 1935, 3569 |
| Mly113I | GGCGCC | 1 cut(s) | 105 |
| MlyI | GAGTC | 5 cut(s) | 556, 593, 1452, 2929, 3805 |
| MmeI | TCCRAC | 2 cut(s) | 851, 4074 |
| Mph1103I | ATGCAT | 2 cut(s) | 2172, 3274 |
| MroI | TCCGGA | 1 cut(s) | 1003 |
| MroXI | GAANNNNTTC | 3 cut(s) | 1856, 3161, 3918 |
| MslI | CAYNNNNRTG | 7 cut(s) | 152, 167, 429, 449, 1841, 2175, 2248 |
| MspA1I | CMGCKG | 3 cut(s) | 914, 2384, 2570 |
| MspI | CCGG | 5 cut(s) | 1004, 2329, 2777, 3434, 3860 |
| MvaI | CCWGG | 7 cut(s) | 102, 953, 1783, 2716, 2913, 3540, 3676 |
| MvnI | CGCG | 3 cut(s) | 344, 346, 743 |
| MwoI | GCNNNNNNNGC | 7 cut(s) | 355, 364, 807, 2780, 2833, 3020, 3605 |
| NarI | GGCGCC | 1 cut(s) | 105 |
| NciI | CCSGG | 3 cut(s) | 2329, 2330, 3860 |
| NcoI | CCATGG | 3 cut(s) | 168, 2272, 3735 |
| NdeI | CATATG | 3 cut(s) | 553, 604, 3456 |
| NmeAIII | GCCGAG | 1 cut(s) | 3748 |
| NmuCI | GTSAC | 6 cut(s) | 5, 596, 955, 965, 2335, 3593 |
| NsbI | TGCGCA | 1 cut(s) | 234 |
| NsiI | ATGCAT | 2 cut(s) | 2172, 3274 |
| NspI | RCATGY | 3 cut(s) | 2170, 2902, 3750 |
| NspV | TTCGAA | 3 cut(s) | 1882, 2346, 3854 |
| OliI | CACNNNNGTG | 1 cut(s) | 152 |
| PagI | TCATGA | 3 cut(s) | 682, 1084, 3868 |
| PaqCI | CACCTGC | 1 cut(s) | 2542 |
| PciI | ACATGT | 1 cut(s) | 3746 |
| PciSI | GCTCTTC | 2 cut(s) | 1522, 2503 |
| PcsI | WCGNNNNNNNCGW | 2 cut(s) | 2245, 2611 |
| PdmI | GAANNNNTTC | 3 cut(s) | 1856, 3161, 3918 |
| PfeI | GAWTC | 7 cut(s) | 1021, 1364, 1598, 1852, 1879, 2692, 3934 |
| Pfl23II | CGTACG | 1 cut(s) | 3938 |
| PflMI | CCANNNNNTGG | 2 cut(s) | 2991, 3472 |
| PfoI | TCCNGGA | 1 cut(s) | 3674 |
| PleI | GAGTC | 5 cut(s) | 556, 593, 1452, 2929, 3804 |
| PluTI | GGCGCC | 1 cut(s) | 108 |
| PpsI | GAGTC | 5 cut(s) | 556, 593, 1452, 2929, 3804 |
| Ppu21I | YACGTR | 1 cut(s) | 2177 |
| PpuMI | RGGWCCY | 1 cut(s) | 1411 |
| PscI | ACATGT | 1 cut(s) | 3746 |
| PshAI | GACNNNNGTC | 1 cut(s) | 930 |
| PshBI | ATTAAT | 1 cut(s) | 1688 |
| PsiI | TTATAA | 1 cut(s) | 1716 |
| Psp124BI | GAGCTC | 1 cut(s) | 1517 |
| Psp5II | RGGWCCY | 1 cut(s) | 1411 |
| Psp6I | CCWGG | 7 cut(s) | 100, 951, 1781, 2714, 2911, 3538, 3674 |
| PspEI | GGTNACC | 1 cut(s) | 2285 |
| PspGI | CCWGG | 7 cut(s) | 100, 951, 1781, 2714, 2911, 3538, 3674 |
| PspLI | CGTACG | 1 cut(s) | 3938 |
| PspPI | GGNCC | 2 cut(s) | 1411, 1895 |
| PspPPI | RGGWCCY | 1 cut(s) | 1411 |
| PstNI | CAGNNNCTG | 1 cut(s) | 917 |
| PsuI | RGATCY | 4 cut(s) | 637, 1487, 1935, 3569 |
| RsaI | GTAC | 7 cut(s) | 859, 1317, 2101, 2267, 2897, 3728, 3940 |
| RsaNI | GTAC | 7 cut(s) | 858, 1316, 2100, 2266, 2896, 3727, 3939 |
| RseI | CAYNNNNRTG | 7 cut(s) | 152, 167, 429, 449, 1841, 2175, 2248 |
| SacI | GAGCTC | 1 cut(s) | 1517 |
| SapI | GCTCTTC | 2 cut(s) | 1522, 2503 |
| Sau96I | GGNCC | 2 cut(s) | 1411, 1895 |
| SchI | GAGTC | 5 cut(s) | 556, 593, 1452, 2929, 3805 |
| SexAI | ACCWGGT | 1 cut(s) | 951 |
| SfaNI | GCATC | 9 cut(s) | 220, 487, 788, 2056, 2210, 3255, 3280, 3367, 3602 |
| SfcI | CTRYAG | 2 cut(s) | 2734, 3388 |
| SfoI | GGCGCC | 1 cut(s) | 106 |
| SfuI | TTCGAA | 3 cut(s) | 1882, 2346, 3854 |
| SinI | GGWCC | 2 cut(s) | 1411, 1895 |
| SmaI | CCCGGG | 1 cut(s) | 2330 |
| SmiMI | CAYNNNNRTG | 7 cut(s) | 152, 167, 429, 449, 1841, 2175, 2248 |
| SmlI | CTYRAG | 4 cut(s) | 851, 1654, 3017, 4054 |
| SmoI | CTYRAG | 4 cut(s) | 851, 1654, 3017, 4054 |
| SspDI | GGCGCC | 1 cut(s) | 104 |
| SspI | AATATT | 2 cut(s) | 1745, 3209 |
| SspMI | CTAG | 4 cut(s) | 2849, 3483, 3609, 3711 |
| SstI | GAGCTC | 1 cut(s) | 1517 |
| StyI | CCWWGG | 8 cut(s) | 168, 942, 1478, 1537, 1623, 2272, 2727, 3735 |
| TaiI | ACGT | 9 cut(s) | 496, 521, 1199, 1210, 1420, 1595, 2179, 2617, 2655 |
| TaqII | GACCGA | 1 cut(s) | 2909 |
| TatI | WGTACW | 2 cut(s) | 857, 2895 |
| TauI | GCSGC | 5 cut(s) | 349, 743, 900, 917, 2822 |
| TfiI | GAWTC | 7 cut(s) | 1021, 1364, 1598, 1852, 1879, 2692, 3934 |
| TscAI | CASTG | 7 cut(s) | 338, 756, 1159, 2590, 2800, 2837, 3703 |
| TseFI | GTSAC | 6 cut(s) | 5, 596, 955, 965, 2335, 3593 |
| Tsp45I | GTSAC | 6 cut(s) | 5, 596, 955, 965, 2335, 3593 |
| TspGWI | ACGGA | 3 cut(s) | 723, 2789, 3889 |
| TspMI | CCCGGG | 1 cut(s) | 2328 |
| TspRI | CASTG | 7 cut(s) | 338, 756, 1159, 2590, 2800, 2837, 3703 |
| Van91I | CCANNNNNTGG | 2 cut(s) | 2991, 3472 |
| VneI | GTGCAC | 4 cut(s) | 1580, 1777, 2241, 3534 |
| VpaK11BI | GGWCC | 2 cut(s) | 1411, 1895 |
| VspI | ATTAAT | 1 cut(s) | 1688 |
| XagI | CCTNNNNNAGG | 3 cut(s) | 1324, 2490, 3391 |
| XapI | RAATTY | 3 cut(s) | 420, 1333, 2228 |
| XceI | RCATGY | 3 cut(s) | 2170, 2902, 3750 |
| XcmI | CCANNNNNNNNNTGG | 2 cut(s) | 175, 1144 |
| XmaI | CCCGGG | 1 cut(s) | 2328 |
| XmnI | GAANNNNTTC | 3 cut(s) | 1856, 3161, 3918 |
| XspI | CTAG | 4 cut(s) | 2849, 3483, 3609, 3711 |
| Zsp2I | ATGCAT | 2 cut(s) | 2172, 3274 |