Calculate codon counts, per-thousand usage, and synonymous codon fractions for DNA sequences.
Paste one or more raw or FASTA-formatted sequences (limit 500,000,000 characters). Only IUPAC DNA characters are retained.
Choose the translation table used to group synonymous codons.
Paste one or more coding sequences in FASTA format. The tool accepts up to 500 million characters and automatically strips non-DNA characters before analysis. Make sure your sequences represent complete or partial coding regions.
Choose the translation table that matches your organism. Use "standard (1)" for most nuclear genes, or select mitochondrial, bacterial, or other specialized codes if your sequences come from those sources. The genetic code determines how synonymous codons are grouped.
Examine the Number column for raw counts, the /1000 column for normalized frequency per thousand codons, and the Fraction column for usage within each synonymous codon family. High fraction values indicate strong codon preference, which is useful for optimizing expression constructs.
The report will note any codons containing ambiguous IUPAC bases or trailing bases that do not form complete triplets. These are excluded from the final counts. Ensure your input sequences are properly trimmed and phased if you want comprehensive codon statistics.
Raw count of each codon within the provided sequence, in the reading frame beginning at the first base.
Frequency of the codon per thousand observed codons, useful for comparing usage bias between sequences.
Proportion of codon usage within its synonymous family. A value near 1 indicates a strong preference for that codon.
Select alternative translation tables to match the organism of interest and see how synonymous codon groupings change.