transposition, RNA-mediated
| Domain Name | Pfam ID | Position | E-value | Description |
|---|---|---|---|---|
| Retrotrans_gag | PF03732 | 120 - 213 | 2.1e-20 | Retrotransposon gag protein |
| RVT_1 | PF00078 | 975 - 1137 | 2.4e-31 | Reverse transcriptase (RNA-dependent DNA polymerase) |
| RT_RNaseH_2 | PF17919 | 1201 - 1299 | 3e-32 | RNase H-like domain found in reverse transcriptase |
| RT_RNaseH | PF17917 | 1226 - 1329 | 2.7e-36 | RNase H-like domain found in reverse transcriptase |
| Integrase_H2C2 | PF17921 | 1417 - 1474 | 1.2e-12 | Integrase zinc binding domain |
| rve | PF00665 | 1495 - 1588 | 1.9e-14 | Integrase core domain |
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) |
|---|---|---|---|
| AanI | TTATAA | 2 cut(s) | 561, 4670 |
| AarI | CACCTGC | 1 cut(s) | 5006 |
| AasI | GACNNNNNNGTC | 1 cut(s) | 2018 |
| AatII | GACGTC | 1 cut(s) | 2263 |
| Acc36I | ACCTGC | 3 cut(s) | 1986, 3038, 5006 |
| AccB1I | GGYRCC | 1 cut(s) | 2878 |
| AccB7I | CCANNNNNTGG | 2 cut(s) | 3379, 4420 |
| AccI | GTMKAC | 2 cut(s) | 1580, 2257 |
| AccIII | TCCGGA | 1 cut(s) | 3673 |
| AciI | CCGC | 5 cut(s) | 107, 2169, 3722, 3839, 4331 |
| AclI | AACGTT | 1 cut(s) | 4855 |
| AcoI | YGGCCR | 2 cut(s) | 3508, 4361 |
| AcuI | CTGAAG | 4 cut(s) | 1613, 2289, 2586, 3636 |
| AcvI | CACGTG | 1 cut(s) | 2753 |
| AcyI | GRCGYC | 1 cut(s) | 2260 |
| AdeI | CACNNNGTG | 1 cut(s) | 4609 |
| AfaI | GTAC | 8 cut(s) | 805, 1531, 2136, 2237, 3151, 4077, 4251, 4614 |
| AfiI | CCNNNNNNNGG | 5 cut(s) | 295, 590, 776, 3379, 4420 |
| AflIII | ACRYGT | 3 cut(s) | 887, 2223, 2750 |
| AgeI | ACCGGT | 1 cut(s) | 2434 |
| AhlI | ACTAGT | 1 cut(s) | 4769 |
| AjnI | CCWGG | 2 cut(s) | 1018, 5191 |
| AjuI | GAANNNNNNNTTGG | 2 cut(s) | 1254, 1286 |
| AleI | CACNNNNGTG | 1 cut(s) | 5237 |
| Alw21I | GWGCWC | 3 cut(s) | 2532, 3327, 4968 |
| Alw26I | GTCTC | 8 cut(s) | 716, 878, 1208, 1596, 4854, 5176, 5315, 5321 |
| Aor13HI | TCCGGA | 1 cut(s) | 3673 |
| AoxI | GGCC | 6 cut(s) | 983, 1106, 2027, 3508, 3639, 4361 |
| ArsI | GACNNNNNNTTYG | 8 cut(s) | 3879, 3911, 4622, 4654, 4674, 4706, 4759, 4791 |
| AseI | ATTAAT | 3 cut(s) | 1467, 1692, 3698 |
| AsiGI | ACCGGT | 1 cut(s) | 2434 |
| Asp700I | GAANNNNTTC | 4 cut(s) | 146, 467, 1674, 2583 |
| AspLEI | GCGC | 1 cut(s) | 5100 |
| AspS9I | GGNCC | 6 cut(s) | 1106, 3115, 3560, 3640, 4508, 5219 |
| AsuC2I | CCSGG | 3 cut(s) | 1857, 4796, 4832 |
| AsuHPI | GGTGA | 8 cut(s) | 578, 979, 1898, 1985, 1987, 2231, 2582, 5030 |
| AsuII | TTCGAA | 1 cut(s) | 5142 |
| AvaII | GGWCC | 4 cut(s) | 3115, 3560, 4508, 5219 |
| BaeGI | GKGCMC | 1 cut(s) | 771 |
| BalI | TGGCCA | 2 cut(s) | 3510, 4363 |
| BamHI | GGATCC | 1 cut(s) | 1852 |
| BanI | GGYRCC | 1 cut(s) | 2878 |
| BanII | GRGCYC | 1 cut(s) | 2532 |
| BbrPI | CACGTG | 1 cut(s) | 2753 |
| BbsI | GAAGAC | 6 cut(s) | 76, 272, 282, 1837, 2739, 3889 |
| Bbv12I | GWGCWC | 3 cut(s) | 2532, 3327, 4968 |
| BceAI | ACGGC | 5 cut(s) | 168, 711, 1802, 3091, 3673 |
| BcgI | CGANNNNNNTGC | 1 cut(s) | 27 |
| BciT130I | CCWGG | 2 cut(s) | 1020, 5193 |
| BclI | TGATCA | 5 cut(s) | 1380, 1888, 3025, 3904, 4600 |
| BcnI | CCSGG | 3 cut(s) | 1857, 4796, 4832 |
| BcoDI | GTCTC | 8 cut(s) | 716, 878, 1208, 1596, 4854, 5176, 5315, 5321 |
| BcuI | ACTAGT | 1 cut(s) | 4769 |
| BfmI | CTRYAG | 4 cut(s) | 204, 625, 666, 2082 |
| BfuAI | ACCTGC | 3 cut(s) | 1986, 3038, 5006 |
| BlpI | GCTNAGC | 2 cut(s) | 401, 3801 |
| BmcAI | AGTACT | 1 cut(s) | 805 |
| Bme1390I | CCNGG | 5 cut(s) | 1020, 1857, 4796, 4832, 5193 |
| Bme18I | GGWCC | 4 cut(s) | 3115, 3560, 4508, 5219 |
| BmgT120I | GGNCC | 6 cut(s) | 1106, 3115, 3560, 3640, 4508, 5219 |
| BmrFI | CCNGG | 5 cut(s) | 1020, 1857, 4796, 4832, 5193 |
| BpiI | GAAGAC | 6 cut(s) | 76, 272, 282, 1837, 2739, 3889 |
| BplI | GAGNNNNNCTC | 4 cut(s) | 841, 873, 3745, 3777 |
| BpmI | CTGGAG | 1 cut(s) | 1569 |
| Bpu1102I | GCTNAGC | 2 cut(s) | 401, 3801 |
| Bpu14I | TTCGAA | 1 cut(s) | 5142 |
| BpuEI | CTTGAG | 7 cut(s) | 1227, 2325, 2516, 3056, 3586, 3620, 5293 |
| BpuMI | CCSGG | 3 cut(s) | 1857, 4796, 4832 |
| BsaAI | YACGTR | 2 cut(s) | 2753, 4079 |
| BsaHI | GRCGYC | 1 cut(s) | 2260 |
| BsaI | GGTCTC | 2 cut(s) | 1208, 4854 |
| BsaWI | WCCGGW | 7 cut(s) | 2434, 3109, 3162, 3673, 3864, 4252, 4951 |
| BsaXI | ACNNNNNCTCC | 5 cut(s) | 2947, 2977, 3640, 3670, 5356 |
| Bsc4I | CCNNNNNNNGG | 5 cut(s) | 295, 590, 776, 3379, 4420 |
| Bse118I | RCCGGY | 2 cut(s) | 2434, 3193 |
| Bse1I | ACTGG | 2 cut(s) | 2588, 2867 |
| Bse3DI | GCAATG | 2 cut(s) | 4219, 5030 |
| BseAI | TCCGGA | 1 cut(s) | 3673 |
| BseBI | CCWGG | 2 cut(s) | 1020, 5193 |
| BseLI | CCNNNNNNNGG | 5 cut(s) | 295, 590, 776, 3379, 4420 |
| BseMI | GCAATG | 2 cut(s) | 4219, 5030 |
| BseMII | CTCAG | 4 cut(s) | 1205, 1650, 3815, 5171 |
| BseNI | ACTGG | 2 cut(s) | 2588, 2867 |
| BseRI | GAGGAG | 4 cut(s) | 792, 849, 1405, 4077 |
| BseSI | GKGCMC | 1 cut(s) | 771 |
| BseYI | CCCAGC | 3 cut(s) | 472, 1543, 1726 |
| BsgI | GTGCAG | 2 cut(s) | 147, 3750 |
| BshFI | GGCC | 6 cut(s) | 985, 1108, 2029, 3510, 3641, 4363 |
| BshNI | GGYRCC | 1 cut(s) | 2878 |
| BshTI | ACCGGT | 1 cut(s) | 2434 |
| BsiHKAI | GWGCWC | 3 cut(s) | 2532, 3327, 4968 |
| BslFI | GGGAC | 5 cut(s) | 331, 915, 2247, 3417, 4521 |
| BslI | CCNNNNNNNGG | 5 cut(s) | 295, 590, 776, 3379, 4420 |
| BsmAI | GTCTC | 8 cut(s) | 716, 878, 1208, 1596, 4854, 5176, 5315, 5321 |
| BsmBI | CGTCTC | 1 cut(s) | 5315 |
| BsmFI | GGGAC | 5 cut(s) | 331, 915, 2247, 3417, 4521 |
| BsmI | GAATGC | 5 cut(s) | 2156, 3174, 4272, 5014, 5083 |
| BsnI | GGCC | 6 cut(s) | 985, 1108, 2029, 3510, 3641, 4363 |
| Bso31I | GGTCTC | 2 cut(s) | 1208, 4854 |
| Bsp119I | TTCGAA | 1 cut(s) | 5142 |
| Bsp1286I | GDGCHC | 4 cut(s) | 771, 2532, 3327, 4968 |
| Bsp13I | TCCGGA | 1 cut(s) | 3673 |
| Bsp1720I | GCTNAGC | 2 cut(s) | 401, 3801 |
| Bsp19I | CCATGG | 2 cut(s) | 589, 5248 |
| BspACI | CCGC | 5 cut(s) | 107, 2169, 3722, 3839, 4331 |
| BspANI | GGCC | 6 cut(s) | 985, 1108, 2029, 3510, 3641, 4363 |
| BspCNI | CTCAG | 4 cut(s) | 1204, 1651, 3814, 5172 |
| BspEI | TCCGGA | 1 cut(s) | 3673 |
| BspHI | TCATGA | 4 cut(s) | 1783, 2314, 3534, 5113 |
| BspMAI | CTGCAG | 2 cut(s) | 208, 2086 |
| BspMI | ACCTGC | 3 cut(s) | 1986, 3038, 5006 |
| BspQI | GCTCTTC | 2 cut(s) | 810, 842 |
| BspT104I | TTCGAA | 1 cut(s) | 5142 |
| BspT107I | GGYRCC | 1 cut(s) | 2878 |
| BspTNI | GGTCTC | 2 cut(s) | 1208, 4854 |
| BsrDI | GCAATG | 2 cut(s) | 4219, 5030 |
| BsrFI | RCCGGY | 2 cut(s) | 2434, 3193 |
| BsrI | ACTGG | 2 cut(s) | 2588, 2867 |
| BssAI | RCCGGY | 2 cut(s) | 2434, 3193 |
| BssNI | GRCGYC | 1 cut(s) | 2260 |
| BssT1I | CCWWGG | 8 cut(s) | 589, 831, 1076, 1340, 1637, 3505, 4091, 5248 |
| Bst2UI | CCWGG | 2 cut(s) | 1020, 5193 |
| Bst4CI | ACNGT | 7 cut(s) | 670, 766, 1623, 2215, 2902, 3484, 4825 |
| Bst6I | CTCTTC | 4 cut(s) | 414, 810, 842, 1800 |
| BstACI | GRCGYC | 1 cut(s) | 2260 |
| BstAPI | GCANNNNNTGC | 2 cut(s) | 104, 3587 |
| BstBAI | YACGTR | 2 cut(s) | 2753, 4079 |
| BstBI | TTCGAA | 1 cut(s) | 5142 |
| BstC8I | GCNNGC | 8 cut(s) | 84, 248, 1905, 2082, 2514, 3837, 4151, 4588 |
| BstDSI | CCRYGG | 3 cut(s) | 589, 2229, 5248 |
| BstEII | GGTNACC | 1 cut(s) | 1973 |
| BstHHI | GCGC | 1 cut(s) | 5100 |
| BstMAI | GTCTC | 8 cut(s) | 716, 878, 1208, 1596, 4854, 5176, 5315, 5321 |
| BstNI | CCWGG | 2 cut(s) | 1020, 5193 |
| BstNSI | RCATGY | 5 cut(s) | 891, 2227, 3615, 4912, 5357 |
| BstPI | GGTNACC | 1 cut(s) | 1973 |
| BstSCI | CCNGG | 5 cut(s) | 1018, 1855, 4794, 4830, 5191 |
| BstSFI | CTRYAG | 4 cut(s) | 204, 625, 666, 2082 |
| BstSLI | GKGCMC | 1 cut(s) | 771 |
| BstV2I | GAAGAC | 6 cut(s) | 76, 272, 282, 1837, 2739, 3889 |
| BstX2I | RGATCY | 3 cut(s) | 348, 1852, 2344 |
| BstXI | CCANNNNNNTGG | 1 cut(s) | 4143 |
| BstYI | RGATCY | 3 cut(s) | 348, 1852, 2344 |
| BsuRI | GGCC | 6 cut(s) | 985, 1108, 2029, 3510, 3641, 4363 |
| BtgI | CCRYGG | 3 cut(s) | 589, 2229, 5248 |
| BtgZI | GCGATG | 1 cut(s) | 4689 |
| BtsI | GCAGTG | 4 cut(s) | 1284, 2537, 2985, 4557 |
| BtsIMutI | CAGTG | 9 cut(s) | 771, 1284, 1819, 2537, 2595, 2985, 3900, 4557, 5364 |
| BveI | ACCTGC | 3 cut(s) | 1986, 3038, 5006 |
| Cac8I | GCNNGC | 8 cut(s) | 84, 248, 1905, 2082, 2514, 3837, 4151, 4588 |
| CciI | TCATGA | 4 cut(s) | 1783, 2314, 3534, 5113 |
| CfoI | GCGC | 1 cut(s) | 5100 |
| Cfr10I | RCCGGY | 2 cut(s) | 2434, 3193 |
| Cfr13I | GGNCC | 6 cut(s) | 1106, 3115, 3560, 3640, 4508, 5219 |
| CseI | GACGC | 1 cut(s) | 3699 |
| Csp6I | GTAC | 8 cut(s) | 804, 1530, 2135, 2236, 3150, 4076, 4250, 4613 |
| CspAI | ACCGGT | 1 cut(s) | 2434 |
| CspCI | CAANNNNNGTGG | 2 cut(s) | 2532, 2567 |
| CviQI | GTAC | 8 cut(s) | 804, 1530, 2135, 2236, 3150, 4076, 4250, 4613 |
| DraI | TTTAAA | 1 cut(s) | 2772 |
| DraIII | CACNNNGTG | 1 cut(s) | 4609 |
| DrdI | GACNNNNNNGTC | 1 cut(s) | 2018 |
| DseDI | GACNNNNNNGTC | 1 cut(s) | 2018 |
| EaeI | YGGCCR | 2 cut(s) | 3508, 4361 |
| Eam1104I | CTCTTC | 4 cut(s) | 414, 810, 842, 1800 |
| EarI | CTCTTC | 4 cut(s) | 414, 810, 842, 1800 |
| Ecl136II | GAGCTC | 1 cut(s) | 2530 |
| Eco130I | CCWWGG | 8 cut(s) | 589, 831, 1076, 1340, 1637, 3505, 4091, 5248 |
| Eco147I | AGGCCT | 1 cut(s) | 985 |
| Eco24I | GRGCYC | 1 cut(s) | 2532 |
| Eco31I | GGTCTC | 2 cut(s) | 1208, 4854 |
| Eco32I | GATATC | 2 cut(s) | 31, 336 |
| Eco47I | GGWCC | 4 cut(s) | 3115, 3560, 4508, 5219 |
| Eco53kI | GAGCTC | 1 cut(s) | 2530 |
| Eco57I | CTGAAG | 4 cut(s) | 1613, 2289, 2586, 3636 |
| Eco72I | CACGTG | 1 cut(s) | 2753 |
| Eco91I | GGTNACC | 1 cut(s) | 1973 |
| EcoICRI | GAGCTC | 1 cut(s) | 2530 |
| EcoO109I | RGGNCCY | 3 cut(s) | 3640, 4508, 5219 |
| EcoO65I | GGTNACC | 1 cut(s) | 1973 |
| EcoRI | GAATTC | 2 cut(s) | 299, 2332 |
| EcoRII | CCWGG | 2 cut(s) | 1018, 5191 |
| EcoRV | GATATC | 2 cut(s) | 31, 336 |
| EcoT14I | CCWWGG | 8 cut(s) | 589, 831, 1076, 1340, 1637, 3505, 4091, 5248 |
| EcoT38I | GRGCYC | 1 cut(s) | 2532 |
| ErhI | CCWWGG | 8 cut(s) | 589, 831, 1076, 1340, 1637, 3505, 4091, 5248 |
| Esp3I | CGTCTC | 1 cut(s) | 5315 |
| FalI | AAGNNNNNCTT | 6 cut(s) | 2184, 2216, 2334, 2366, 3819, 3851 |
| FaqI | GGGAC | 5 cut(s) | 331, 915, 2247, 3417, 4521 |
| FauNDI | CATATG | 1 cut(s) | 311 |
| FbaI | TGATCA | 5 cut(s) | 1380, 1888, 3025, 3904, 4600 |
| FblI | GTMKAC | 2 cut(s) | 1580, 2257 |
| FriOI | GRGCYC | 1 cut(s) | 2532 |
| GlaI | GCGC | 1 cut(s) | 5099 |
| GsaI | CCCAGC | 3 cut(s) | 476, 1547, 1730 |
| GsuI | CTGGAG | 1 cut(s) | 1569 |
| HaeIII | GGCC | 6 cut(s) | 985, 1108, 2029, 3510, 3641, 4363 |
| HgaI | GACGC | 1 cut(s) | 3699 |
| HhaI | GCGC | 1 cut(s) | 5100 |
| Hin1I | GRCGYC | 1 cut(s) | 2260 |
| Hin6I | GCGC | 1 cut(s) | 5098 |
| HinP1I | GCGC | 1 cut(s) | 5098 |
| HincII | GTYRAC | 5 cut(s) | 961, 1933, 2258, 3436, 5306 |
| HindII | GTYRAC | 5 cut(s) | 961, 1933, 2258, 3436, 5306 |
| HindIII | AAGCTT | 6 cut(s) | 244, 679, 714, 1967, 2417, 2813 |
| HpaI | GTTAAC | 1 cut(s) | 1933 |
| HphI | GGTGA | 8 cut(s) | 578, 979, 1898, 1985, 1987, 2231, 2582, 5030 |
| Hpy99I | CGWCG | 3 cut(s) | 15, 2262, 3715 |
| HpyCH4III | ACNGT | 7 cut(s) | 670, 766, 1623, 2215, 2902, 3484, 4825 |
| HpyCH4IV | ACGT | 7 cut(s) | 1528, 2260, 2752, 4078, 4438, 4855, 5308 |
| HpySE526I | ACGT | 7 cut(s) | 1528, 2260, 2752, 4078, 4438, 4855, 5308 |
| Hsp92I | GRCGYC | 1 cut(s) | 2260 |
| HspAI | GCGC | 1 cut(s) | 5098 |
| Kpn2I | TCCGGA | 1 cut(s) | 3673 |
| Ksp22I | TGATCA | 5 cut(s) | 1380, 1888, 3025, 3904, 4600 |
| KspAI | GTTAAC | 1 cut(s) | 1933 |
| LguI | GCTCTTC | 2 cut(s) | 810, 842 |
| MaeII | ACGT | 7 cut(s) | 1528, 2260, 2752, 4078, 4438, 4855, 5308 |
| MaeIII | GTNAC | 7 cut(s) | 1973, 2219, 3185, 4120, 4439, 4744, 5230 |
| MfeI | CAATTG | 8 cut(s) | 1110, 1881, 2676, 4064, 4232, 4581, 4902, 5256 |
| MflI | RGATCY | 3 cut(s) | 348, 1852, 2344 |
| MhlI | GDGCHC | 4 cut(s) | 771, 2532, 3327, 4968 |
| MlsI | TGGCCA | 2 cut(s) | 3510, 4363 |
| MluNI | TGGCCA | 2 cut(s) | 3510, 4363 |
| MlyI | GAGTC | 6 cut(s) | 1598, 1827, 2477, 3781, 5075, 5178 |
| MmeI | TCCRAC | 7 cut(s) | 792, 1004, 2806, 2933, 3255, 3693, 4941 |
| Mox20I | TGGCCA | 2 cut(s) | 3510, 4363 |
| MroI | TCCGGA | 1 cut(s) | 3673 |
| MroXI | GAANNNNTTC | 4 cut(s) | 146, 467, 1674, 2583 |
| MscI | TGGCCA | 2 cut(s) | 3510, 4363 |
| MslI | CAYNNNNRTG | 3 cut(s) | 2228, 4293, 5237 |
| Msp20I | TGGCCA | 2 cut(s) | 3510, 4363 |
| MspA1I | CMGCKG | 3 cut(s) | 2171, 4331, 5038 |
| MspR9I | CCNGG | 5 cut(s) | 1020, 1857, 4796, 4832, 5193 |
| MunI | CAATTG | 8 cut(s) | 1110, 1881, 2676, 4064, 4232, 4581, 4902, 5256 |
| Mva1269I | GAATGC | 5 cut(s) | 2156, 3174, 4272, 5014, 5083 |
| MvaI | CCWGG | 2 cut(s) | 1020, 5193 |
| NciI | CCSGG | 3 cut(s) | 1857, 4796, 4832 |
| NcoI | CCATGG | 2 cut(s) | 589, 5248 |
| NdeI | CATATG | 1 cut(s) | 311 |
| NmuCI | GTSAC | 5 cut(s) | 1973, 2219, 4439, 4744, 5230 |
| NspI | RCATGY | 5 cut(s) | 891, 2227, 3615, 4912, 5357 |
| NspV | TTCGAA | 1 cut(s) | 5142 |
| OliI | CACNNNNGTG | 1 cut(s) | 5237 |
| PagI | TCATGA | 4 cut(s) | 1783, 2314, 3534, 5113 |
| PaqCI | CACCTGC | 1 cut(s) | 5006 |
| PceI | AGGCCT | 1 cut(s) | 985 |
| PciI | ACATGT | 2 cut(s) | 887, 2223 |
| PciSI | GCTCTTC | 2 cut(s) | 810, 842 |
| PcsI | WCGNNNNNNNCGW | 2 cut(s) | 3958, 4414 |
| PctI | GAATGC | 5 cut(s) | 2156, 3174, 4272, 5014, 5083 |
| PdmI | GAANNNNTTC | 4 cut(s) | 146, 467, 1674, 2583 |
| PfeI | GAWTC | 9 cut(s) | 1081, 1472, 1487, 1535, 2294, 2318, 2444, 2721, 4082 |
| PflMI | CCANNNNNTGG | 2 cut(s) | 3379, 4420 |
| PinAI | ACCGGT | 1 cut(s) | 2434 |
| PleI | GAGTC | 6 cut(s) | 1597, 1827, 2476, 3781, 5074, 5178 |
| PmaCI | CACGTG | 1 cut(s) | 2753 |
| PmlI | CACGTG | 1 cut(s) | 2753 |
| PpsI | GAGTC | 6 cut(s) | 1597, 1827, 2476, 3781, 5074, 5178 |
| Ppu21I | YACGTR | 2 cut(s) | 2753, 4079 |
| PpuMI | RGGWCCY | 2 cut(s) | 4508, 5219 |
| PscI | ACATGT | 2 cut(s) | 887, 2223 |
| PshBI | ATTAAT | 3 cut(s) | 1467, 1692, 3698 |
| PsiI | TTATAA | 2 cut(s) | 561, 4670 |
| Psp124BI | GAGCTC | 1 cut(s) | 2532 |
| Psp1406I | AACGTT | 1 cut(s) | 4855 |
| Psp5II | RGGWCCY | 2 cut(s) | 4508, 5219 |
| Psp6I | CCWGG | 2 cut(s) | 1018, 5191 |
| PspCI | CACGTG | 1 cut(s) | 2753 |
| PspEI | GGTNACC | 1 cut(s) | 1973 |
| PspFI | CCCAGC | 3 cut(s) | 472, 1543, 1726 |
| PspGI | CCWGG | 2 cut(s) | 1018, 5191 |
| PspPI | GGNCC | 6 cut(s) | 1106, 3115, 3560, 3640, 4508, 5219 |
| PspPPI | RGGWCCY | 2 cut(s) | 4508, 5219 |
| PstI | CTGCAG | 2 cut(s) | 208, 2086 |
| PsuI | RGATCY | 3 cut(s) | 348, 1852, 2344 |
| PvuII | CAGCTG | 1 cut(s) | 5038 |
| RsaI | GTAC | 8 cut(s) | 805, 1531, 2136, 2237, 3151, 4077, 4251, 4614 |
| RsaNI | GTAC | 8 cut(s) | 804, 1530, 2135, 2236, 3150, 4076, 4250, 4613 |
| RseI | CAYNNNNRTG | 3 cut(s) | 2228, 4293, 5237 |
| SacI | GAGCTC | 1 cut(s) | 2532 |
| SalI | GTCGAC | 1 cut(s) | 2256 |
| SapI | GCTCTTC | 2 cut(s) | 810, 842 |
| Sau96I | GGNCC | 6 cut(s) | 1106, 3115, 3560, 3640, 4508, 5219 |
| SbfI | CCTGCAGG | 1 cut(s) | 208 |
| ScaI | AGTACT | 1 cut(s) | 805 |
| SchI | GAGTC | 6 cut(s) | 1598, 1827, 2477, 3781, 5075, 5178 |
| ScrFI | CCNGG | 5 cut(s) | 1020, 1857, 4796, 4832, 5193 |
| SdaI | CCTGCAGG | 1 cut(s) | 208 |
| SduI | GDGCHC | 4 cut(s) | 771, 2532, 3327, 4968 |
| SfcI | CTRYAG | 4 cut(s) | 204, 625, 666, 2082 |
| SfuI | TTCGAA | 1 cut(s) | 5142 |
| SinI | GGWCC | 4 cut(s) | 3115, 3560, 4508, 5219 |
| SmiMI | CAYNNNNRTG | 3 cut(s) | 2228, 4293, 5237 |
| SmlI | CTYRAG | 7 cut(s) | 1242, 2340, 2531, 3035, 3565, 3635, 5272 |
| SmoI | CTYRAG | 7 cut(s) | 1242, 2340, 2531, 3035, 3565, 3635, 5272 |
| SpeI | ACTAGT | 1 cut(s) | 4769 |
| Sse8387I | CCTGCAGG | 1 cut(s) | 208 |
| SseBI | AGGCCT | 1 cut(s) | 985 |
| SsiI | CCGC | 5 cut(s) | 107, 2169, 3722, 3839, 4331 |
| SspI | AATATT | 6 cut(s) | 1696, 3923, 4462, 4636, 4727, 4810 |
| SstI | GAGCTC | 1 cut(s) | 2532 |
| StuI | AGGCCT | 1 cut(s) | 985 |
| StyD4I | CCNGG | 5 cut(s) | 1018, 1855, 4794, 4830, 5191 |
| StyI | CCWWGG | 8 cut(s) | 589, 831, 1076, 1340, 1637, 3505, 4091, 5248 |
| TaaI | ACNGT | 7 cut(s) | 670, 766, 1623, 2215, 2902, 3484, 4825 |
| TaiI | ACGT | 7 cut(s) | 1531, 2263, 2755, 4081, 4441, 4858, 5311 |
| TaqI | TCGA | 5 cut(s) | 13, 2257, 3952, 5142, 5176 |
| TaqII | GACCGA | 1 cut(s) | 2028 |
| TatI | WGTACW | 2 cut(s) | 803, 2235 |
| TauI | GCSGC | 2 cut(s) | 110, 4334 |
| TfiI | GAWTC | 9 cut(s) | 1081, 1472, 1487, 1535, 2294, 2318, 2444, 2721, 4082 |
| TscAI | CASTG | 9 cut(s) | 771, 1291, 1819, 2544, 2595, 2992, 3907, 4557, 5371 |
| TseFI | GTSAC | 5 cut(s) | 1973, 2219, 4439, 4744, 5230 |
| Tsp45I | GTSAC | 5 cut(s) | 1973, 2219, 4439, 4744, 5230 |
| TspGWI | ACGGA | 3 cut(s) | 341, 2218, 3950 |
| TspRI | CASTG | 9 cut(s) | 771, 1291, 1819, 2544, 2595, 2992, 3907, 4557, 5371 |
| Van91I | CCANNNNNTGG | 2 cut(s) | 3379, 4420 |
| VpaK11BI | GGWCC | 4 cut(s) | 3115, 3560, 4508, 5219 |
| VspI | ATTAAT | 3 cut(s) | 1467, 1692, 3698 |
| XbaI | TCTAGA | 3 cut(s) | 2818, 3616, 3853 |
| XceI | RCATGY | 5 cut(s) | 891, 2227, 3615, 4912, 5357 |
| XmiI | GTMKAC | 2 cut(s) | 1580, 2257 |
| XmnI | GAANNNNTTC | 4 cut(s) | 146, 467, 1674, 2583 |
| ZraI | GACGTC | 1 cut(s) | 2261 |
| ZrmI | AGTACT | 1 cut(s) | 805 |