DNA GC content and base composition
GC content is the fraction of sequence bases that are guanine or cytosine, expressed as a percentage of all counted DNA bases.
This calculator accepts unambiguous A, T, G, and C bases. It ignores whitespace and FASTA header lines beginning with >, but rejects ambiguity symbols so the denominator is never silently redefined.
How to calculate GC percentage
- Paste DNA: Enter A, T, G, and C or paste FASTA containing header lines and sequence.
- Check ambiguity codes: Resolve or remove N and other IUPAC ambiguity symbols before calculation.
- Calculate: Review GC percentage and the counted base totals.
- Preserve context: Record the sequence coordinates, strand, and source when using the result analytically.
Formula and variables
Every accepted nucleotide contributes once to the denominator; G and C contribute to the numerator.
GC% = (G count + C count) / total A,T,G,C count × 100- G — Guanine count
- Number of G bases (bases)
- C — Cytosine count
- Number of C bases (bases)
- N — Sequence length
- Total accepted A, T, G, and C bases (bases)
Twelve-base sequence
Calculate GC content for ATGCGCGTATGC.
- Sequence
- ATGCGCGTATGC
- G + C = 8
- Total bases = 12
- GC% = 8/12 × 100
Result: GC content is 66.67%.
Eight of the twelve unambiguous bases are G or C.
Understanding your results
GC percentage is descriptive
GC content summarizes composition but does not identify sequence order or biological function.
- Sequences with identical GC percentages can have very different arrangements.
- Local windows can differ substantially from whole-sequence GC content.
- Primer behavior and melting temperature depend on more than GC percentage alone.
Assumptions
- The input represents DNA using A, T, G, and C.
- All accepted bases have equal weight in the composition percentage.
- FASTA header lines begin with > on their own lines.
Limitations
- Rejects ambiguous IUPAC nucleotide codes rather than assigning fractional counts.
- Does not calculate RNA composition, melting temperature, molecular weight, or sliding-window GC.
- Does not validate biological origin, sequence orientation, or coordinate range.
Common mistakes
- Including FASTA metadata in the sequence count.
- Silently deleting ambiguous bases and changing the denominator.
- Using GC percentage alone as a melting-temperature prediction.
- Comparing regions of different coordinates without recording sequence scope.
Practical use cases
Sequence screening
Inspect the overall composition of a short DNA sequence or FASTA record.
Teaching base composition
Connect nucleotide counts with a percentage calculation.
Frequently asked questions
Does the calculator accept FASTA?
Yes. It ignores lines whose first non-space character is > and removes whitespace from the remaining sequence.
How are N bases handled?
They are rejected. This avoids silently choosing whether N belongs in the denominator.
Is GC content the same as melting temperature?
No. GC content can influence duplex stability, but melting temperature also depends on sequence, length, salt, concentration, and the selected thermodynamic model.
Sources and review
- Base Composition — National Library of Medicine MeSH. Accessed 2026-07-13.
- Deoxyribonucleic Acid (DNA) Fact Sheet — National Human Genome Research Institute. Accessed 2026-07-13.
Reviewed 2026-07-13.