Every organism spreads its synonymous codon choices differently, and that choice decides how well a designed sequence expresses in a given host. These are the 26 reference tables Nucleora optimizes against, computed from RefSeq coding sequences, with the statistics that matter for design.
The spread here is not cosmetic. The two mycobacteria average 77.6% GC at third positions while the vertebrates average 54.5%, and that gap is why a sequence tuned for one host reads poorly in the other. Effective codon number runs from 41.4 to 56.4: the low end means an organism concentrates on a narrow set of preferred codons, the high end means it uses most of them.
Click any column heading to sort. GC3 is the mean frequency of a G or C at the third position across multi-codon amino acid families; Nc is Wright's effective number of codons, where 61 would mean no bias at all.
| Organism | GC3 | Nc | CDS | Group |
|---|---|---|---|---|
| M. tuberculosisMycobacterium tuberculosis | 41.4 | 472 | Pathogens (antigen source) | |
| M. bovis (bovine/elephant TB)Mycobacterium bovis | 41.7 | 1,229 | Pathogens (antigen source) | |
| Bottlenose dolphinTursiops truncatus | 49.3 | 250 | Other mammals | |
| Green anole (lizard)Anolis carolinensis | 52.1 | 250 | Reference / lab | |
| CheetahAcinonyx jubatus | 53.0 | 250 | Big cats | |
| Red foxVulpes vulpes | 52.5 | 250 | Wildlife carnivores (oral-bait targets) | |
| Rhesus macaqueMacaca mulatta | 52.9 | 248 | Primates | |
| SheepOvis aries | 52.9 | 250 | Hoofstock / livestock | |
| PigSus scrofa | 53.2 | 250 | Hoofstock / livestock | |
| CatFelis catus | 52.9 | 248 | Carnivores / companion | |
| DogCanis lupus familiaris | 53.4 | 248 | Carnivores / companion | |
| Polar bearUrsus maritimus | 54.5 | 248 | Conservation / megafauna | |
| White rhinocerosCeratotherium simum | 53.5 | 201 | Conservation / megafauna | |
| KoalaPhascolarctos cinereus | 55.2 | 250 | Other mammals | |
| AxolotlAmbystoma mexicanum | 53.6 | 247 | Reptiles & amphibians | |
| CattleBos taurus | 55.5 | 250 | Hoofstock / livestock | |
| ChimpanzeePan troglodytes | 54.5 | 241 | Primates | |
| HorseEquus caballus | 55.2 | 249 | Hoofstock / livestock | |
| Giant pandaAiluropoda melanoleuca | 55.6 | 247 | Conservation / megafauna | |
| TigerPanthera tigris | 56.2 | 249 | Big cats | |
| LionPanthera leo | 56.4 | 250 | Big cats | |
| African elephantLoxodonta africana | 54.7 | 248 | Conservation / megafauna | |
| California condorGymnogyps californianus | 55.6 | 250 | Birds | |
| Western gorillaGorilla gorilla | 55.9 | 250 | Primates | |
| Asian elephantElephas maximus | 55.4 | 250 | Conservation / megafauna | |
| FerretMustela putorius furo | 55.2 | 248 | Carnivores / companion |
For each organism, RefSeq coding sequences were counted codon by codon, and each codon's count divided by the total for its amino acid. That makes every number below a statement about synonymous choice rather than about amino-acid composition. Tables built on fewer than 100 coding sequences were left out entirely rather than published with a caveat, because at that sample size the frequencies are noise.
Each organism page states which NCBI translation table its frequencies describe. For the vertebrates that is the standard nuclear code, and those tables must not be applied to mitochondrial genes, where four codons carry different meanings.
Nucleora codon-optimizes a coding sequence against any of these organisms, folds the result with ViennaRNA, and reports where secondary structure would interfere.
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