Decode coding sequences and inspect codon choices. Track amino acid counts, codons, and GC shifts. Turn raw sequence data into clear, exportable insight today.
This sample shows how a short coding region might look after analysis.
| RNA Codon | DNA Codon | Amino Acid | Count | Freq % | Per 1000 | RSCU |
|---|---|---|---|---|---|---|
| AUG | ATG | Methionine (M) | 8 | 8.000 | 80.000 | 1.000 |
| GCU | GCT | Alanine (A) | 12 | 12.000 | 120.000 | 1.600 |
| GCC | GCC | Alanine (A) | 6 | 6.000 | 60.000 | 0.800 |
| GCA | GCA | Alanine (A) | 4 | 4.000 | 40.000 | 0.533 |
| GCG | GCG | Alanine (A) | 8 | 8.000 | 80.000 | 1.067 |
| UUU | TTT | Phenylalanine (F) | 10 | 10.000 | 100.000 | 1.250 |
| UUC | TTC | Phenylalanine (F) | 6 | 6.000 | 60.000 | 0.750 |
| GGA | GGA | Glycine (G) | 9 | 9.000 | 90.000 | 1.200 |
| GGC | GGC | Glycine (G) | 5 | 5.000 | 50.000 | 0.667 |
| UGA | TGA | Stop (*) | 1 | 1.000 | 10.000 | 1.000 |
Codon count
Codon Count = number of exact appearances of a codon in the analyzed reading frame.
Frequency percentage
Frequency % = (Codon Count ÷ Total Normalized Codons) × 100.
Per-1000 frequency
Per 1000 = (Codon Count ÷ Total Normalized Codons) × 1000.
RSCU
RSCU = Observed Codon Count ÷ (Total counts for synonymous codons ÷ Number of synonymous codons).
GC content
GC % = ((G + C) nucleotides ÷ analyzed nucleotide length) × 100.
GC3 content
GC3 % = ((G or C at third codon positions) ÷ total raw codons) × 100.
It shows how often each codon appears in a coding sequence. That helps reveal synonymous preferences, translational bias, sequence composition, and possible optimization opportunities for expression studies.
Codons are read in triplets. Shifting the frame changes every codon boundary, which can completely alter counts, amino acid interpretation, stop codon positions, and derived statistics.
RSCU means Relative Synonymous Codon Usage. A value near 1 suggests equal synonymous use, above 1 suggests preference, and below 1 suggests underrepresentation within that amino acid family.
Usually, codon usage comparisons focus on sense codons, so stops are excluded. Including them can still be useful when you want complete triplet composition across an entire coding region.
Yes. It accepts both. DNA thymine is converted internally to RNA uracil for codon mapping, while the results table still displays matching DNA and RNA codons side by side.
A valid codon needs three nucleotides. If the final sequence segment has one or two leftover bases after framing, they cannot form a complete codon and are excluded.
Not directly. This page reports codon statistics from your sequence itself. Host-based optimization usually needs an external reference table, weighting scheme, or organism-specific codon bias dataset.
GC3 is the GC percentage at third codon positions only. It is useful because wobble positions often vary more and can strongly reflect mutational pressure or codon preference patterns.
Important Note: All the Calculators listed in this site are for educational purpose only and we do not guarentee the accuracy of results. Please do consult with other sources as well.