GC content — the share of a DNA sequence made up of guanine and cytosine — is one of the most basic descriptors of a piece of DNA, but it shows up everywhere from PCR primer design to genome-wide comparisons between species. This calculator counts bases, computes GC% and AT%, and shows the full composition so you can read a sequence at a glance.

Why GC content matters in molecular biology

Each base pair in DNA is held together by hydrogen bonds: G pairs with C using three hydrogen bonds, while A pairs with T using only two. That one extra bond means GC-rich DNA is more thermally stable and has a higher melting temperature than AT-rich DNA of the same length — which is exactly why GC content is a standard input to PCR primer design, probe design, and predicting how a sequence will behave under heat or denaturing conditions.

GC content also varies widely across organisms and even across regions of the same genome — some bacterial genomes sit above 70% GC while others sit below 30%, and within a single genome, coding regions and regulatory regions often differ in GC content from the surrounding sequence. That variation makes GC content a useful quick signal in genome annotation, species identification, and comparative genomics.

How ambiguous bases are handled

Real-world sequence data isn't always a clean string of A, T, G, and C. FASTA files, sequencing reads, and consensus sequences often include IUPAC ambiguity codes like N (any base), R, Y, S, W, K, or M (each representing two possible bases), especially where a sequencing result was uncertain. This calculator counts every character you paste, but only A, T, G, and C ever contribute to the GC% and AT% denominator — everything else is tallied separately as "other / ambiguous" so it never silently skews the percentages.

The tool is also case-insensitive and strips all whitespace before counting, so pasting a FASTA-formatted sequence with line breaks (after removing the ">" header line) works exactly the same as pasting one continuous string.

Limits of this tool

This calculator is a quick composition and GC% check, not a full bioinformatics suite — it doesn't align sequences, detect CpG islands, or compute a sliding-window GC plot across a long genome. The melting-temperature estimate uses the simple Wallace rule, which is most accurate for short oligos (roughly under 14 nucleotides) and increasingly approximate for longer sequences, where salt-adjusted or nearest-neighbor thermodynamic models are more accurate. For primer design or lab work, cross-check results with dedicated primer-design or sequence-analysis software.