Mitochondrial protein
| Domain Name | Pfam ID | Position | E-value | Description |
|---|---|---|---|---|
| Retrotran_gag_2 | PF14223 | 73 - 233 | 4.4e-25 | gag-polypeptide of LTR copia-type |
| Pol_BBD | PF22936 | 336 - 414 | 1.6e-23 | Pol polyprotein, beta-barrel domain |
| gag_pre-integrs | PF13976 | 453 - 512 | 2.5e-13 | GAG-pre-integrase domain |
| rve | PF00665 | 527 - 627 | 6.9e-13 | Integrase core domain |
| SH3_retrovirus | PF25597 | 701 - 764 | 1.2e-24 | Retroviral polymerase SH3-like domain |
| RVT_2 | PF07727 | 873 - 1117 | 1.5e-86 | Reverse transcriptase (RNA-dependent DNA polymerase) |
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) |
|---|---|---|---|
| Acc36I | ACCTGC | 2 cut(s) | 3474, 3749 |
| Acc65I | GGTACC | 1 cut(s) | 1957 |
| AccB1I | GGYRCC | 3 cut(s) | 138, 1957, 2558 |
| AccB7I | CCANNNNNTGG | 1 cut(s) | 1407 |
| AccBSI | CCGCTC | 1 cut(s) | 1041 |
| AccI | GTMKAC | 1 cut(s) | 1278 |
| AccIII | TCCGGA | 1 cut(s) | 3451 |
| AciI | CCGC | 8 cut(s) | 1041, 1869, 1880, 1982, 2562, 2874, 3787, 3969 |
| AclWI | GGATC | 5 cut(s) | 1401, 1538, 2207, 2561, 2684 |
| AcoI | YGGCCR | 1 cut(s) | 3492 |
| AcsI | RAATTY | 6 cut(s) | 112, 307, 579, 2717, 3224, 3567 |
| AcuI | CTGAAG | 6 cut(s) | 47, 252, 317, 464, 3612, 4031 |
| AcvI | CACGTG | 2 cut(s) | 1566, 2390 |
| AdeI | CACNNNGTG | 1 cut(s) | 2393 |
| AfiI | CCNNNNNNNGG | 3 cut(s) | 1292, 1407, 2023 |
| AflIII | ACRYGT | 2 cut(s) | 2322, 2904 |
| AgeI | ACCGGT | 1 cut(s) | 2555 |
| AhlI | ACTAGT | 1 cut(s) | 2432 |
| AjiI | CACGTC | 1 cut(s) | 2905 |
| AjnI | CCWGG | 3 cut(s) | 1192, 3026, 3352 |
| AleI | CACNNNNGTG | 2 cut(s) | 518, 1377 |
| Alw21I | GWGCWC | 4 cut(s) | 105, 1028, 2443, 2703 |
| Alw26I | GTCTC | 4 cut(s) | 1301, 2313, 2798, 3250 |
| Alw44I | GTGCAC | 1 cut(s) | 2439 |
| AlwI | GGATC | 5 cut(s) | 1401, 1538, 2207, 2561, 2684 |
| AlwNI | CAGNNNCTG | 3 cut(s) | 442, 3073, 3740 |
| Aor13HI | TCCGGA | 1 cut(s) | 3451 |
| AoxI | GGCC | 4 cut(s) | 843, 1973, 3024, 3492 |
| ApaLI | GTGCAC | 1 cut(s) | 2439 |
| ApoI | RAATTY | 6 cut(s) | 112, 307, 579, 2717, 3224, 3567 |
| AsiGI | ACCGGT | 1 cut(s) | 2555 |
| Asp700I | GAANNNNTTC | 2 cut(s) | 452, 1077 |
| Asp718I | GGTACC | 1 cut(s) | 1957 |
| AspLEI | GCGC | 3 cut(s) | 238, 264, 1935 |
| AspS9I | GGNCC | 3 cut(s) | 360, 1613, 1992 |
| AsuII | TTCGAA | 2 cut(s) | 368, 3048 |
| AsuNHI | GCTAGC | 2 cut(s) | 428, 3796 |
| AvaII | GGWCC | 3 cut(s) | 360, 1613, 1992 |
| AxyI | CCTNAGG | 1 cut(s) | 1977 |
| BaeGI | GKGCMC | 1 cut(s) | 2443 |
| BalI | TGGCCA | 1 cut(s) | 3494 |
| BanI | GGYRCC | 3 cut(s) | 138, 1957, 2558 |
| BanII | GRGCYC | 1 cut(s) | 105 |
| BarI | GAAGNNNNNNTAC | 2 cut(s) | 942, 974 |
| BauI | CACGAG | 2 cut(s) | 1928, 3000 |
| BbrPI | CACGTG | 2 cut(s) | 1566, 2390 |
| BbsI | GAAGAC | 4 cut(s) | 226, 261, 2268, 2907 |
| Bbv12I | GWGCWC | 4 cut(s) | 105, 1028, 2443, 2703 |
| BccI | CCATC | 9 cut(s) | 71, 71, 1111, 1290, 1462, 2167, 2271, 2339, 3938 |
| BceAI | ACGGC | 1 cut(s) | 2226 |
| BcgI | CGANNNNNNTGC | 8 cut(s) | 2644, 2678, 2765, 2799, 3038, 3072, 3106, 3140 |
| BciT130I | CCWGG | 3 cut(s) | 1194, 3028, 3354 |
| BciVI | GTATCC | 2 cut(s) | 70, 74 |
| BclI | TGATCA | 2 cut(s) | 730, 3979 |
| BcoDI | GTCTC | 4 cut(s) | 1301, 2313, 2798, 3250 |
| BcuI | ACTAGT | 1 cut(s) | 2432 |
| BfaI | CTAG | 7 cut(s) | 429, 1013, 1397, 2433, 3599, 3797, 4075 |
| BfmI | CTRYAG | 3 cut(s) | 1165, 1454, 3753 |
| BfuAI | ACCTGC | 2 cut(s) | 3474, 3749 |
| BfuI | GTATCC | 2 cut(s) | 70, 74 |
| BglII | AGATCT | 1 cut(s) | 459 |
| BmcAI | AGTACT | 1 cut(s) | 3652 |
| Bme1390I | CCNGG | 3 cut(s) | 1194, 3028, 3354 |
| Bme18I | GGWCC | 3 cut(s) | 360, 1613, 1992 |
| BmgBI | CACGTC | 1 cut(s) | 2905 |
| BmgT120I | GGNCC | 3 cut(s) | 360, 1613, 1992 |
| BmiI | GGNNCC | 5 cut(s) | 140, 1010, 1959, 2560, 3917 |
| BmrFI | CCNGG | 3 cut(s) | 1194, 3028, 3354 |
| BmsI | GCATC | 6 cut(s) | 1093, 1245, 2116, 2374, 3774, 3873 |
| BmtI | GCTAGC | 2 cut(s) | 432, 3800 |
| BoxI | GACNNNNGTC | 1 cut(s) | 2154 |
| BpiI | GAAGAC | 4 cut(s) | 226, 261, 2268, 2907 |
| BplI | GAGNNNNNCTC | 2 cut(s) | 32, 64 |
| BpmI | CTGGAG | 5 cut(s) | 39, 109, 1360, 1608, 3165 |
| Bpu14I | TTCGAA | 2 cut(s) | 368, 3048 |
| BsaAI | YACGTR | 4 cut(s) | 1566, 1787, 2390, 3929 |
| BsaI | GGTCTC | 1 cut(s) | 1301 |
| BsaJI | CCNNGG | 4 cut(s) | 414, 846, 1193, 2022 |
| BsaWI | WCCGGW | 6 cut(s) | 1960, 2044, 2507, 2555, 3451, 3877 |
| BsaXI | ACNNNNNCTCC | 8 cut(s) | 2039, 2042, 2069, 2072, 3138, 3168, 3228, 3258 |
| Bsc4I | CCNNNNNNNGG | 3 cut(s) | 1292, 1407, 2023 |
| Bse118I | RCCGGY | 2 cut(s) | 1416, 2555 |
| Bse1I | ACTGG | 6 cut(s) | 56, 98, 157, 1377, 2789, 3148 |
| Bse21I | CCTNAGG | 1 cut(s) | 1977 |
| Bse3DI | GCAATG | 2 cut(s) | 3807, 3964 |
| BseAI | TCCGGA | 1 cut(s) | 3451 |
| BseBI | CCWGG | 3 cut(s) | 1194, 3028, 3354 |
| BseDI | CCNNGG | 4 cut(s) | 414, 846, 1193, 2022 |
| BseLI | CCNNNNNNNGG | 3 cut(s) | 1292, 1407, 2023 |
| BseMI | GCAATG | 2 cut(s) | 3807, 3964 |
| BseNI | ACTGG | 6 cut(s) | 56, 98, 157, 1377, 2789, 3148 |
| BseRI | GAGGAG | 5 cut(s) | 813, 1812, 1815, 2063, 2384 |
| BseSI | GKGCMC | 1 cut(s) | 2443 |
| BseYI | CCCAGC | 1 cut(s) | 4045 |
| BsgI | GTGCAG | 1 cut(s) | 1291 |
| BshFI | GGCC | 4 cut(s) | 845, 1975, 3026, 3494 |
| BshNI | GGYRCC | 3 cut(s) | 138, 1957, 2558 |
| BshTI | ACCGGT | 1 cut(s) | 2555 |
| BsiHKAI | GWGCWC | 4 cut(s) | 105, 1028, 2443, 2703 |
| BsiSI | CCGG | 7 cut(s) | 1417, 1961, 2045, 2508, 2556, 3452, 3878 |
| BslI | CCNNNNNNNGG | 3 cut(s) | 1292, 1407, 2023 |
| BsmAI | GTCTC | 4 cut(s) | 1301, 2313, 2798, 3250 |
| BsmBI | CGTCTC | 1 cut(s) | 2798 |
| BsmI | GAATGC | 2 cut(s) | 2041, 2362 |
| BsnI | GGCC | 4 cut(s) | 845, 1975, 3026, 3494 |
| Bso31I | GGTCTC | 1 cut(s) | 1301 |
| Bsp119I | TTCGAA | 2 cut(s) | 368, 3048 |
| Bsp1286I | GDGCHC | 4 cut(s) | 105, 1028, 2443, 2703 |
| Bsp13I | TCCGGA | 1 cut(s) | 3451 |
| Bsp1407I | TGTACA | 3 cut(s) | 2958, 3462, 3573 |
| Bsp19I | CCATGG | 1 cut(s) | 846 |
| BspACI | CCGC | 8 cut(s) | 1041, 1869, 1880, 1982, 2562, 2874, 3787, 3969 |
| BspANI | GGCC | 4 cut(s) | 845, 1975, 3026, 3494 |
| BspEI | TCCGGA | 1 cut(s) | 3451 |
| BspHI | TCATGA | 2 cut(s) | 2550, 3976 |
| BspLI | GGNNCC | 5 cut(s) | 140, 1010, 1959, 2560, 3917 |
| BspMAI | CTGCAG | 1 cut(s) | 3757 |
| BspMI | ACCTGC | 2 cut(s) | 3474, 3749 |
| BspOI | GCTAGC | 2 cut(s) | 432, 3800 |
| BspPI | GGATC | 5 cut(s) | 1401, 1538, 2207, 2561, 2684 |
| BspQI | GCTCTTC | 2 cut(s) | 365, 2523 |
| BspT104I | TTCGAA | 2 cut(s) | 368, 3048 |
| BspT107I | GGYRCC | 3 cut(s) | 138, 1957, 2558 |
| BspTNI | GGTCTC | 1 cut(s) | 1301 |
| BsrBI | CCGCTC | 1 cut(s) | 1041 |
| BsrDI | GCAATG | 2 cut(s) | 3807, 3964 |
| BsrFI | RCCGGY | 2 cut(s) | 1416, 2555 |
| BsrGI | TGTACA | 3 cut(s) | 2958, 3462, 3573 |
| BsrI | ACTGG | 6 cut(s) | 56, 98, 157, 1377, 2789, 3148 |
| BssAI | RCCGGY | 2 cut(s) | 1416, 2555 |
| BssECI | CCNNGG | 4 cut(s) | 414, 846, 1193, 2022 |
| BssNAI | GTATAC | 1 cut(s) | 1279 |
| BssSI | CACGAG | 2 cut(s) | 1928, 3000 |
| BssT1I | CCWWGG | 3 cut(s) | 414, 846, 2022 |
| Bst1107I | GTATAC | 1 cut(s) | 1279 |
| Bst2BI | CACGAG | 2 cut(s) | 1928, 3000 |
| Bst2UI | CCWGG | 3 cut(s) | 1194, 3028, 3354 |
| Bst4CI | ACNGT | 8 cut(s) | 205, 658, 1693, 2077, 2204, 2809, 2984, 3467 |
| BstAPI | GCANNNNNTGC | 1 cut(s) | 3764 |
| BstAUI | TGTACA | 3 cut(s) | 2958, 3462, 3573 |
| BstBAI | YACGTR | 4 cut(s) | 1566, 1787, 2390, 3929 |
| BstBI | TTCGAA | 2 cut(s) | 368, 3048 |
| BstC8I | GCNNGC | 6 cut(s) | 13, 430, 434, 438, 1245, 3798 |
| BstDSI | CCRYGG | 1 cut(s) | 846 |
| BstENI | CCTNNNNNAGG | 1 cut(s) | 1290 |
| BstHHI | GCGC | 3 cut(s) | 238, 264, 1935 |
| BstMAI | GTCTC | 4 cut(s) | 1301, 2313, 2798, 3250 |
| BstNI | CCWGG | 3 cut(s) | 1194, 3028, 3354 |
| BstNSI | RCATGY | 3 cut(s) | 621, 2114, 2326 |
| BstPAI | GACNNNNGTC | 1 cut(s) | 2154 |
| BstSCI | CCNGG | 3 cut(s) | 1192, 3026, 3352 |
| BstSFI | CTRYAG | 3 cut(s) | 1165, 1454, 3753 |
| BstSLI | GKGCMC | 1 cut(s) | 2443 |
| BstSNI | TACGTA | 1 cut(s) | 1787 |
| BstV2I | GAAGAC | 4 cut(s) | 226, 261, 2268, 2907 |
| BstX2I | RGATCY | 4 cut(s) | 459, 1393, 1543, 2676 |
| BstXI | CCANNNNNNTGG | 2 cut(s) | 2759, 3006 |
| BstYI | RGATCY | 4 cut(s) | 459, 1393, 1543, 2676 |
| BstZ17I | GTATAC | 1 cut(s) | 1279 |
| Bsu36I | CCTNAGG | 1 cut(s) | 1977 |
| BsuI | GTATCC | 2 cut(s) | 70, 74 |
| BsuRI | GGCC | 4 cut(s) | 845, 1975, 3026, 3494 |
| BtgI | CCRYGG | 1 cut(s) | 846 |
| BtrI | CACGTC | 1 cut(s) | 2905 |
| BtsI | GCAGTG | 2 cut(s) | 1411, 2034 |
| BtsIMutI | CAGTG | 9 cut(s) | 91, 440, 1384, 1411, 2034, 2188, 2796, 3472, 4007 |
| BveI | ACCTGC | 2 cut(s) | 3474, 3749 |
| Cac8I | GCNNGC | 6 cut(s) | 13, 430, 434, 438, 1245, 3798 |
| CaiI | CAGNNNCTG | 3 cut(s) | 442, 3073, 3740 |
| CciI | TCATGA | 2 cut(s) | 2550, 3976 |
| CfoI | GCGC | 3 cut(s) | 238, 264, 1935 |
| Cfr10I | RCCGGY | 2 cut(s) | 1416, 2555 |
| Cfr13I | GGNCC | 3 cut(s) | 360, 1613, 1992 |
| CspAI | ACCGGT | 1 cut(s) | 2555 |
| CspCI | CAANNNNNGTGG | 6 cut(s) | 189, 224, 2472, 2507, 3996, 4031 |
| DraI | TTTAAA | 2 cut(s) | 1732, 3175 |
| DraIII | CACNNNGTG | 1 cut(s) | 2393 |
| EaeI | YGGCCR | 1 cut(s) | 3492 |
| Ecl136II | GAGCTC | 1 cut(s) | 103 |
| Eco105I | TACGTA | 1 cut(s) | 1787 |
| Eco130I | CCWWGG | 3 cut(s) | 414, 846, 2022 |
| Eco147I | AGGCCT | 1 cut(s) | 3026 |
| Eco24I | GRGCYC | 1 cut(s) | 105 |
| Eco31I | GGTCTC | 1 cut(s) | 1301 |
| Eco32I | GATATC | 1 cut(s) | 2365 |
| Eco47I | GGWCC | 3 cut(s) | 360, 1613, 1992 |
| Eco53kI | GAGCTC | 1 cut(s) | 103 |
| Eco57I | CTGAAG | 6 cut(s) | 47, 252, 317, 464, 3612, 4031 |
| Eco72I | CACGTG | 2 cut(s) | 1566, 2390 |
| Eco81I | CCTNAGG | 1 cut(s) | 1977 |
| EcoICRI | GAGCTC | 1 cut(s) | 103 |
| EcoNI | CCTNNNNNAGG | 1 cut(s) | 1290 |
| EcoO109I | RGGNCCY | 1 cut(s) | 360 |
| EcoRII | CCWGG | 3 cut(s) | 1192, 3026, 3352 |
| EcoRV | GATATC | 1 cut(s) | 2365 |
| EcoT14I | CCWWGG | 3 cut(s) | 414, 846, 2022 |
| EcoT22I | ATGCAT | 2 cut(s) | 1260, 3888 |
| EcoT38I | GRGCYC | 1 cut(s) | 105 |
| ErhI | CCWWGG | 3 cut(s) | 414, 846, 2022 |
| Esp3I | CGTCTC | 1 cut(s) | 2798 |
| FalI | AAGNNNNNCTT | 4 cut(s) | 437, 469, 2663, 2695 |
| FauI | CCCGC | 1 cut(s) | 1887 |
| FauNDI | CATATG | 2 cut(s) | 377, 1035 |
| FbaI | TGATCA | 2 cut(s) | 730, 3979 |
| FblI | GTMKAC | 1 cut(s) | 1278 |
| FriOI | GRGCYC | 1 cut(s) | 105 |
| FspBI | CTAG | 7 cut(s) | 429, 1013, 1397, 2433, 3599, 3797, 4075 |
| GlaI | GCGC | 3 cut(s) | 237, 263, 1934 |
| GsaI | CCCAGC | 1 cut(s) | 4049 |
| GsuI | CTGGAG | 5 cut(s) | 39, 109, 1360, 1608, 3165 |
| HaeIII | GGCC | 4 cut(s) | 845, 1975, 3026, 3494 |
| HapII | CCGG | 7 cut(s) | 1417, 1961, 2045, 2508, 2556, 3452, 3878 |
| HhaI | GCGC | 3 cut(s) | 238, 264, 1935 |
| Hin6I | GCGC | 3 cut(s) | 236, 262, 1933 |
| HinP1I | GCGC | 3 cut(s) | 236, 262, 1933 |
| HincII | GTYRAC | 4 cut(s) | 565, 661, 1200, 1226 |
| HindII | GTYRAC | 4 cut(s) | 565, 661, 1200, 1226 |
| HindIII | AAGCTT | 6 cut(s) | 29, 872, 1583, 2963, 3177, 3282 |
| HpaII | CCGG | 7 cut(s) | 1417, 1961, 2045, 2508, 2556, 3452, 3878 |
| HpyCH4III | ACNGT | 8 cut(s) | 205, 658, 1693, 2077, 2204, 2809, 2984, 3467 |
| HpyCH4IV | ACGT | 5 cut(s) | 1565, 1786, 2389, 2904, 3928 |
| HpySE526I | ACGT | 5 cut(s) | 1565, 1786, 2389, 2904, 3928 |
| HspAI | GCGC | 3 cut(s) | 236, 262, 1933 |
| Kpn2I | TCCGGA | 1 cut(s) | 3451 |
| KpnI | GGTACC | 1 cut(s) | 1961 |
| Ksp22I | TGATCA | 2 cut(s) | 730, 3979 |
| LguI | GCTCTTC | 2 cut(s) | 365, 2523 |
| LmnI | GCTCC | 9 cut(s) | 58, 128, 1840, 1940, 2485, 3001, 3087, 3552, 3683 |
| LweI | GCATC | 6 cut(s) | 1093, 1245, 2116, 2374, 3774, 3873 |
| MaeI | CTAG | 7 cut(s) | 429, 1013, 1397, 2433, 3599, 3797, 4075 |
| MaeII | ACGT | 5 cut(s) | 1565, 1786, 2389, 2904, 3928 |
| MaeIII | GTNAC | 9 cut(s) | 555, 745, 857, 866, 1159, 1433, 3326, 3356, 3718 |
| MbiI | CCGCTC | 1 cut(s) | 1041 |
| MflI | RGATCY | 4 cut(s) | 459, 1393, 1543, 2676 |
| MhlI | GDGCHC | 4 cut(s) | 105, 1028, 2443, 2703 |
| MlsI | TGGCCA | 1 cut(s) | 3494 |
| MluNI | TGGCCA | 1 cut(s) | 3494 |
| MmeI | TCCRAC | 4 cut(s) | 185, 923, 2841, 3996 |
| Mox20I | TGGCCA | 1 cut(s) | 3494 |
| Mph1103I | ATGCAT | 2 cut(s) | 1260, 3888 |
| MroI | TCCGGA | 1 cut(s) | 3451 |
| MroXI | GAANNNNTTC | 2 cut(s) | 452, 1077 |
| MscI | TGGCCA | 1 cut(s) | 3494 |
| MslI | CAYNNNNRTG | 8 cut(s) | 518, 1377, 1507, 1919, 2163, 2549, 3906, 3908 |
| Msp20I | TGGCCA | 1 cut(s) | 3494 |
| MspA1I | CMGCKG | 2 cut(s) | 25, 2564 |
| MspI | CCGG | 7 cut(s) | 1417, 1961, 2045, 2508, 2556, 3452, 3878 |
| MspR9I | CCNGG | 3 cut(s) | 1194, 3028, 3354 |
| Mva1269I | GAATGC | 2 cut(s) | 2041, 2362 |
| MvaI | CCWGG | 3 cut(s) | 1194, 3028, 3354 |
| NcoI | CCATGG | 1 cut(s) | 846 |
| NdeI | CATATG | 2 cut(s) | 377, 1035 |
| NheI | GCTAGC | 2 cut(s) | 428, 3796 |
| NlaIV | GGNNCC | 5 cut(s) | 140, 1010, 1959, 2560, 3917 |
| NmeAIII | GCCGAG | 1 cut(s) | 2707 |
| NmuCI | GTSAC | 6 cut(s) | 555, 866, 1159, 1433, 3356, 3718 |
| NsiI | ATGCAT | 2 cut(s) | 1260, 3888 |
| NspI | RCATGY | 3 cut(s) | 621, 2114, 2326 |
| NspV | TTCGAA | 2 cut(s) | 368, 3048 |
| OliI | CACNNNNGTG | 2 cut(s) | 518, 1377 |
| PagI | TCATGA | 2 cut(s) | 2550, 3976 |
| PceI | AGGCCT | 1 cut(s) | 3026 |
| PciI | ACATGT | 1 cut(s) | 2322 |
| PciSI | GCTCTTC | 2 cut(s) | 365, 2523 |
| PcsI | WCGNNNNNNNCGW | 1 cut(s) | 3045 |
| PctI | GAATGC | 2 cut(s) | 2041, 2362 |
| PdmI | GAANNNNTTC | 2 cut(s) | 452, 1077 |
| PflMI | CCANNNNNTGG | 1 cut(s) | 1407 |
| PinAI | ACCGGT | 1 cut(s) | 2555 |
| PmaCI | CACGTG | 2 cut(s) | 1566, 2390 |
| PmlI | CACGTG | 2 cut(s) | 1566, 2390 |
| Ppu21I | YACGTR | 4 cut(s) | 1566, 1787, 2390, 3929 |
| PpuMI | RGGWCCY | 1 cut(s) | 360 |
| PscI | ACATGT | 1 cut(s) | 2322 |
| PshAI | GACNNNNGTC | 1 cut(s) | 2154 |
| Psp124BI | GAGCTC | 1 cut(s) | 105 |
| Psp5II | RGGWCCY | 1 cut(s) | 360 |
| Psp6I | CCWGG | 3 cut(s) | 1192, 3026, 3352 |
| PspCI | CACGTG | 2 cut(s) | 1566, 2390 |
| PspFI | CCCAGC | 1 cut(s) | 4045 |
| PspGI | CCWGG | 3 cut(s) | 1192, 3026, 3352 |
| PspN4I | GGNNCC | 5 cut(s) | 140, 1010, 1959, 2560, 3917 |
| PspPI | GGNCC | 3 cut(s) | 360, 1613, 1992 |
| PspPPI | RGGWCCY | 1 cut(s) | 360 |
| PsrI | GAACNNNNNNTAC | 2 cut(s) | 2942, 2974 |
| PstI | CTGCAG | 1 cut(s) | 3757 |
| PstNI | CAGNNNCTG | 3 cut(s) | 442, 3073, 3740 |
| PsuI | RGATCY | 4 cut(s) | 459, 1393, 1543, 2676 |
| PvuII | CAGCTG | 1 cut(s) | 25 |
| RseI | CAYNNNNRTG | 8 cut(s) | 518, 1377, 1507, 1919, 2163, 2549, 3906, 3908 |
| SacI | GAGCTC | 1 cut(s) | 105 |
| SapI | GCTCTTC | 2 cut(s) | 365, 2523 |
| Sau96I | GGNCC | 3 cut(s) | 360, 1613, 1992 |
| ScaI | AGTACT | 1 cut(s) | 3652 |
| ScrFI | CCNGG | 3 cut(s) | 1194, 3028, 3354 |
| SduI | GDGCHC | 4 cut(s) | 105, 1028, 2443, 2703 |
| SfaNI | GCATC | 6 cut(s) | 1093, 1245, 2116, 2374, 3774, 3873 |
| SfcI | CTRYAG | 3 cut(s) | 1165, 1454, 3753 |
| SfuI | TTCGAA | 2 cut(s) | 368, 3048 |
| SinI | GGWCC | 3 cut(s) | 360, 1613, 1992 |
| SmiMI | CAYNNNNRTG | 8 cut(s) | 518, 1377, 1507, 1919, 2163, 2549, 3906, 3908 |
| SnaBI | TACGTA | 1 cut(s) | 1787 |
| SpeI | ACTAGT | 1 cut(s) | 2432 |
| SseBI | AGGCCT | 1 cut(s) | 3026 |
| SsiI | CCGC | 8 cut(s) | 1041, 1869, 1880, 1982, 2562, 2874, 3787, 3969 |
| SspMI | CTAG | 7 cut(s) | 429, 1013, 1397, 2433, 3599, 3797, 4075 |
| SstI | GAGCTC | 1 cut(s) | 105 |
| StuI | AGGCCT | 1 cut(s) | 3026 |
| StyD4I | CCNGG | 3 cut(s) | 1192, 3026, 3352 |
| StyI | CCWWGG | 3 cut(s) | 414, 846, 2022 |
| TaaI | ACNGT | 8 cut(s) | 205, 658, 1693, 2077, 2204, 2809, 2984, 3467 |
| TaiI | ACGT | 5 cut(s) | 1568, 1789, 2392, 2907, 3931 |
| TaqII | GACCGA | 1 cut(s) | 1630 |
| TatI | WGTACW | 5 cut(s) | 2958, 3462, 3573, 3650, 3827 |
| TauI | GCSGC | 1 cut(s) | 2564 |
| TscAI | CASTG | 9 cut(s) | 98, 447, 1384, 1418, 2034, 2188, 2796, 3472, 4014 |
| TseFI | GTSAC | 6 cut(s) | 555, 866, 1159, 1433, 3356, 3718 |
| Tsp45I | GTSAC | 6 cut(s) | 555, 866, 1159, 1433, 3356, 3718 |
| TspGWI | ACGGA | 2 cut(s) | 1918, 2718 |
| TspRI | CASTG | 9 cut(s) | 98, 447, 1384, 1418, 2034, 2188, 2796, 3472, 4014 |
| Van91I | CCANNNNNTGG | 1 cut(s) | 1407 |
| VneI | GTGCAC | 1 cut(s) | 2439 |
| VpaK11BI | GGWCC | 3 cut(s) | 360, 1613, 1992 |
| XagI | CCTNNNNNAGG | 1 cut(s) | 1290 |
| XapI | RAATTY | 6 cut(s) | 112, 307, 579, 2717, 3224, 3567 |
| XceI | RCATGY | 3 cut(s) | 621, 2114, 2326 |
| XmiI | GTMKAC | 1 cut(s) | 1278 |
| XmnI | GAANNNNTTC | 2 cut(s) | 452, 1077 |
| XspI | CTAG | 7 cut(s) | 429, 1013, 1397, 2433, 3599, 3797, 4075 |
| ZrmI | AGTACT | 1 cut(s) | 3652 |
| Zsp2I | ATGCAT | 2 cut(s) | 1260, 3888 |