GC content is the share of a DNA or RNA sequence made of guanine (G) and cytosine (C) bases, written as a percentage. For the sequence ATGCGC, four of the six bases are G or C, so the GC content is 4 divided by 6 times 100, which is 66.7%. The remaining bases are adenine and thymine (or uracil in RNA), counted as the AT content. GC and AT together cover every valid base in the strand.

How is GC percentage calculated?

The formula is GC% equals (count of G plus count of C) divided by the total sequence length, times 100. The tool counts each base after cleaning out spaces, line breaks, digits and FASTA header lines. For example GCGC gives 4 of 4 G or C, so 100%; ATAT gives 0 of 4, so 0%; and the balanced ATGC gives 2 of 4, so exactly 50%. Invalid symbols stay in the denominator so the figure stays honest.

Why does GC content matter?

A guanine-cytosine pair is held by three hydrogen bonds, while an adenine-thymine pair has only two, so a GC-rich duplex is more thermally stable and melts at a higher temperature. This matters for PCR primer design, where you usually aim for a GC content of roughly 40% to 60% and a matched melting temperature across a primer pair. GC content also varies between organisms and gene regions, so it is a quick fingerprint of a sequence.

What is melting temperature (Tm) and how is it estimated here?

The melting temperature is the point at which half of a double-stranded sequence separates into single strands. For short oligonucleotides of 13 bases or fewer the tool uses the Wallace rule: Tm equals 4 times the count of G plus C, plus 2 times the count of A plus T. So the 4-mer ATGC gives 4 times 2 plus 2 times 2, which is 12°C. Longer sequences switch to a salt-independent simplified formula based on GC fraction and length.

What is the Wallace rule?

The Wallace rule, also called the 2-plus-4 rule, is a quick melting-temperature estimate for short primers: Tm equals 2°C for every A or T base plus 4°C for every G or C base. It assumes standard salt conditions and works well up to about 13 to 14 bases, which is why this tool uses it only for short oligos and a nearest-neighbour-style simplified formula for longer sequences where the Wallace rule overestimates.

Can I paste FASTA format or RNA?

Yes. Any line beginning with the > header marker is dropped, so you can paste a whole FASTA record and only the sequence is read. Spaces, tabs, line breaks and digits are ignored too. For RNA, the tool counts U (uracil) and groups it with A and T on the AT side, since U pairs like T. Mixed case is fine because every letter is folded to uppercase before counting.

Design PCR primers in the right GC window

You are ordering a primer pair and want both in the 40% to 60% GC band with matched melting temperatures. Paste each candidate primer, read its GC% and Wallace Tm side by side, and adjust the sequence until the two primers melt within a couple of degrees of each other. The short-oligo Wallace estimate is exactly the rule of thumb most primer-design guides reach for first.

Sanity-check a sequence pulled from GenBank

You copied a gene region out of a FASTA file and want a quick profile before loading it into heavier software. Paste the whole record, header line and all, and the tool ignores the header, reports the GC content and base composition, and flags any N or ambiguity codes that slipped in. It is a 5-second check that the sequence is what you think it is.

Teach or learn base composition in a genetics class

A student needs to see why GCGC is 100% GC and ATAT is 0% before the idea of GC-driven stability clicks. Type short sequences, watch the percentage and the per-base counts update live, and switch a T to a G to see the Tm climb. The shareable URL lets an instructor send a worked example that opens with the sequence already loaded.

Compare GC content across organisms or gene regions

Bacterial genomes range from roughly 25% to 75% GC, and that difference shows up in codon usage and stability. Paste sequences from different sources one after another, copy each GC% report, and line them up to see the spread. Because everything is client-side you can run through dozens of sequences without a rate limit or an upload.

GC Content Calculator — DNA & RNA GC Percentage and Tm

Paste a DNA or RNA sequence and get GC%, AT%, per-base counts, length and a melting-temperature estimate. FASTA headers and spaces are ignored, invalid bases flagged, all in your browser.

Runs locally
Category Calculator
Best for Getting a realistic range before a purchase, plan, workout, or schedule decision.

DNA / RNA sequence

Paste raw letters or a FASTA block. Spaces, line breaks, digits and ">" header lines are ignored.

Enter a sequence to see its GC content.

What this tool does

A GC content calculator for molecular biology, built to run fully in your browser. Paste any DNA or RNA sequence, raw letters or a whole FASTA block, and it reports the GC percentage, the AT percentage, a per-base count of A, C, G, T and U, the cleaned sequence length, and a melting temperature estimate. The cleaner strips spaces, line breaks, digits and every line that starts with a FASTA header marker, then folds the rest to uppercase, so a sequence copied straight out of GenBank or a primer order form needs no hand editing first. Anything that is not A, C, G, T or U after cleaning is counted separately as an invalid base and shown in the composition table, so an ambiguity code or a stray typo never silently skews your percentage. GC content drives primer design, PCR annealing temperature, and the thermal stability of a duplex, and this tool gives you all of those readings at once with a one-click copyable report and a shareable link. No sequence ever leaves the page.

Tool details

Input: Files + Text; The page exposes text boxes, numeric controls, file pickers, or structured inputs depending on the tool.
Output: Live result + Copy; The result area focuses on usable output, with copy, download, or preview actions when supported.
Privacy: Browser-side processing; The main tool logic does not call an external API, so inputs normally stay in the current tab.
Save / share: Shareable URL state; Key settings are encoded in the URL so another person can reopen the same setup.
Performance budget: Initial JS <= 9 KB; No WASM budget is declared, keeping the tool quick to open on mobile.
Best fit: Calculator · Student; Category and role tags drive related tools, internal links, and quick fit checks.

How to use

1. Input

Paste or drop your content into the tool panel.
2. Process

Click the button. All processing is local in your browser.
3. Copy / Download

Copy the result or download to disk in one click.

How GC Content Calculator fits into your work

Use it for fast estimates, comparisons, and planning numbers before you make the final call.

Calculation jobs

Getting a realistic range before a purchase, plan, workout, or schedule decision.
Comparing scenarios by changing one input at a time.
Turning rough assumptions into a number you can discuss.

Calculation checks

Double-check units, dates, rates, and rounding assumptions.
Treat health, finance, tax, and legal outputs as planning aids, not professional advice.
Save the inputs that produced an important result so you can reproduce it later.

Good next steps

These links move the current task into a more complete workflow.

Real-world use cases

Design PCR primers in the right GC window
You are ordering a primer pair and want both in the 40% to 60% GC band with matched melting temperatures. Paste each candidate primer, read its GC% and Wallace Tm side by side, and adjust the sequence until the two primers melt within a couple of degrees of each other. The short-oligo Wallace estimate is exactly the rule of thumb most primer-design guides reach for first.
Sanity-check a sequence pulled from GenBank
You copied a gene region out of a FASTA file and want a quick profile before loading it into heavier software. Paste the whole record, header line and all, and the tool ignores the header, reports the GC content and base composition, and flags any N or ambiguity codes that slipped in. It is a 5-second check that the sequence is what you think it is.
Teach or learn base composition in a genetics class
A student needs to see why GCGC is 100% GC and ATAT is 0% before the idea of GC-driven stability clicks. Type short sequences, watch the percentage and the per-base counts update live, and switch a T to a G to see the Tm climb. The shareable URL lets an instructor send a worked example that opens with the sequence already loaded.
Compare GC content across organisms or gene regions
Bacterial genomes range from roughly 25% to 75% GC, and that difference shows up in codon usage and stability. Paste sequences from different sources one after another, copy each GC% report, and line them up to see the spread. Because everything is client-side you can run through dozens of sequences without a rate limit or an upload.

Common pitfalls

Forgetting that invalid bases stay in the denominator. If your sequence has an N or an ambiguity code, it is counted as "other" and included in the total length, so a sequence full of Ns will read a lower GC% than the valid bases alone. Check the invalid-base flag before trusting the percentage.
Using the short-oligo Wallace Tm for a long sequence. The Wallace rule is reliable only up to about 13 to 14 bases; past that it overestimates badly. This tool switches formulas automatically, but if you copy a Wallace number from elsewhere for a 40-mer, it will be wrong.
Pasting a sequence with the FASTA header still treated as bases. In some tools the > line and its description letters get counted as bases and ruin the result. Here header lines are dropped, but if you paste a description without the > marker, those letters will be counted as invalid bases.

Privacy

Every step of the analysis, the cleaning, the base counting, the GC and AT percentages and the melting-temperature estimate, is plain JavaScript that runs in your browser tab. The sequence you paste is never uploaded and never logged. The one caveat: the shareable link encodes your sequence in the URL query string, so a link pasted into chat will record that sequence in the recipient server access log. For an unpublished or proprietary sequence, use the copy button and paste the report text rather than sharing the URL.

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GC Content Calculator — DNA & RNA GC Percentage and Tm

What this tool does

Tool details

How to use

1. Input

2. Process

3. Copy / Download

How GC Content Calculator fits into your work

Calculation jobs

Calculation checks

Good next steps

Real-world use cases

Design PCR primers in the right GC window

Sanity-check a sequence pulled from GenBank

Teach or learn base composition in a genetics class

Compare GC content across organisms or gene regions

Common pitfalls

Privacy

FAQ

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