GC Content Calculator

What is GC content?

GC content is the share of a DNA or RNA sequence made up of guanine (G) and cytosine (C).

GC content (%) = (count of G + count of C) / total base count × 100

For example, if 3 out of 10 bases are G and 2 are C, GC content is 50%. Depending on the organism or genomic region, GC content typically ranges anywhere from the low 20s to the high 70s (percent).

Why does GC content matter?

G-C base pairs are held together by three hydrogen bonds, while A-T pairs have only two — so higher GC content generally means a more thermally stable double helix. That single property is why GC content shows up across a range of practical bioinformatics tasks.

• PCR primer design: higher GC content raises melting temperature (Tm), so checking a primer's GC content (commonly recommended in the 40–60% range) helps predict binding stability.
• Genome and species characterization: organisms tend to have a characteristic average GC content (for example, Mycobacterium tuberculosis is GC-rich while Plasmodium falciparum is strongly AT-rich), which can be a useful clue when identifying the likely source of an unknown sequence or spotting contamination.
• Sequencing quality control: next-generation sequencing (NGS) is prone to coverage bias in regions with extreme GC content, so knowing GC content ahead of time helps with interpreting coverage results.
• Gene prediction and comparative genomics: gene-dense regions within a genome often differ in GC content from gene-poor regions, making it a useful supporting signal for gene prediction and isochore analysis.

What is GC skew?

GC skew is computed as (G - C) / (G + C) and captures the relative imbalance between G and C on a single strand. A positive value means more G, a negative value means more C. In organisms with circular genomes, such as bacteria, the sign of GC skew often flips near the origin and terminus of replication, which makes it a useful signal for locating the origin of replication. This tool reports AT skew ((A-T)/(A+T)) alongside GC skew for the same reason.

Sliding window analysis

A single average GC value hides local variation within a sequence. This tool slides a window of a size you choose across the sequence and computes the GC content of each window, plotting the result as a chart. That makes it easy to spot local regions of unusually high or low GC content — such as CpG islands, regulatory regions, or repetitive elements. Use a smaller window for finer detail, or a larger one to see the broad trend.

Multi-FASTA support

Paste an input with multiple > headers and the tool summarizes GC content, AT content, and GC skew for every record in a table. Click a table row, or pick a sequence from the dropdown above, to switch the detailed stats and sliding-window chart to that record.

How to use it

1. Paste your DNA/RNA sequence (or a FASTA / multi-FASTA block) into the input box above.
2. Adjust the sliding window size if you want a finer or coarser view of the chart.
3. If you pasted multiple sequences, pick the one you want from the table or dropdown.
4. Copy the report or download it as a text file.

Frequently asked questions