About the GC Content Calculator
This GC content calculator counts the bases in a DNA or RNA sequence and reports the share that are guanine (G) or cytosine (C). Paste plain sequence or FASTA — header lines starting with “>”, spaces, line breaks and numbers are ignored, and upper- or lower-case letters both work.
GC content matters because G–C pairs are held by three hydrogen bonds versus two for A–T, so GC-rich DNA is more stable and melts at a higher temperature. Molecular biologists check it when designing PCR primers (40–60% is the usual target), choosing probes, comparing genomes, or troubleshooting difficult templates.
The ambiguity code S (G or C) counts toward GC and W (A or T) toward AT; other IUPAC codes such as N, R or Y are counted separately and excluded from the percentage. The melting temperature shown is a quick textbook estimate, not a nearest-neighbour calculation — use a dedicated primer Tm tool for final primer design.
With the default inputs, the gc content is 51.61%. Change any value above to recalculate instantly.
How to use the gc content calculator
- 1Paste your DNA or RNA sequence, with or without a FASTA header.
- 2Read the GC percentage and the AT/AU percentage.
- 3Check the base counts and any ambiguous bases flagged.
- 4Use the GC skew and basic Tm as quick quality checks for primers or probes.
Formula and method
GC content is the fraction of nucleotides that are guanine or cytosine. The calculator strips FASTA headers, whitespace and digits, counts each base, and divides G + C by the number of bases whose identity is known to be either GC or AT (U replaces T in RNA). The ambiguity code S counts as GC and W as AT; codes that mix GC and AT possibilities, such as N, R or Y, are reported but left out of the percentage.
GC skew compares the two strands’ composition and is used to locate replication origins in bacterial genomes. The melting-temperature estimate uses the Wallace rule, Tm = 2(A+T) + 4(G+C), for sequences under 14 nt and Tm = 64.9 + 41 × (G+C − 16.4) ÷ N for longer ones — simple textbook approximations.
- G, C, A, T
- Counts of each nucleotide (U counted with T for RNA)
- N
- Number of unambiguous bases (for the Tm estimate)
- Tm
- Approximate melting temperature (°C)
Worked examples
31-nt DNA fragment
The sequence has 8 G, 8 C, 7 A and 8 T. GC = 16 ÷ 31 = 51.61%. With 31 bases the long-sequence formula gives Tm ≈ 64.9 + 41 × (16 − 16.4) ÷ 31 = 64.4 °C.
FASTA input with lower case and N bases
The header line is skipped and case is ignored. Of 15 known bases, 10 are G or C, so GC = 66.67%. The two N bases are counted in the length (17) but excluded from the percentage.
RNA sequence
U is treated like T. There are 7 G and 5 C out of 21 bases, giving 57.14% GC, and a GC skew of (7 − 5) ÷ 12 = 0.167.
Frequently asked questions
What is GC content?+
GC content is the percentage of bases in a DNA or RNA molecule that are guanine or cytosine. Because G–C pairs form three hydrogen bonds rather than two, higher GC content makes the double helix more thermally stable.
What is a good GC content for PCR primers?+
Primers are usually designed with 40–60% GC, ideally with a G or C at the 3′ end (a “GC clamp”) but no more than three G/C in the last five bases. This balances binding strength against non-specific priming.
What is the GC content of the human genome?+
The human genome averages roughly 41% GC, but it varies widely between regions: gene-rich areas and CpG islands near promoters are much more GC-rich than gene-poor regions.
How are N and other ambiguous bases handled?+
IUPAC ambiguity codes that could be either a GC or an AT base (N, R, Y, K, M, B, D, H, V) are counted in the length and reported separately but are excluded from the GC percentage, because their identity is unknown. S is counted as GC and W as AT.
What does GC skew tell you?+
GC skew, (G − C)/(G + C), measures strand asymmetry. In bacterial genomes it changes sign at the origin and terminus of replication, so cumulative skew plots are used to find them.