Codon Usage Frequency Calculator

Paste a complete coding sequence when possible. FASTA headers are ignored automatically, DNA T is converted to RNA U internally, and incomplete trailing bases are reported but not counted.

Choose the reading frame that matches your CDS. If the frame is wrong, stop codons and unusual codon usage can appear even when the biological sequence is valid.

Select a reference host when you want to compare your sequence with an expression system. Rare and low flags are based on the host synonymous codon fraction, so they are best read as screening signals rather than optimization instructions.

Frequency per 1,000 normalizes codon counts so sequences of different lengths can be compared. Synonymous fraction compares codons that encode the same amino acid.

GC3 reports how often the third codon position is G or C. It is useful for spotting third-position bias, which often changes across organisms and expression hosts.

For organism-level reference tables, use the codon usage frequency table. For translation checks, use the DNA to protein converter.