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GC Content Calculator

Paste a DNA or RNA sequence to get its GC content, AT content, length and the count of each base. FASTA headers and whitespace are ignored.

Formula

GC %=G+CA+C+G+T×100\mathrm{GC}\,\% = \dfrac{G + C}{A + C + G + T}\times 100
A, C, G, TA,\ C,\ G,\ T
number of each base in the sequence (U counts as T for RNA)

How it works

GC content is the share of bases that are guanine or cytosine. G pairs with C through three hydrogen bonds and A with T through two, and GC-rich sequences also stack more favourably, so a higher GC content makes a duplex harder to separate.

Characters that are not A, C, G, T or U, such as N or other ambiguity codes, are left out of the percentage and reported separately rather than guessed.

Worked example

A 39-nucleotide sequence containing 9 A, 8 C, 14 G and 8 T.

  1. G + C = 14 + 8 = 22.
  2. GC% = 22 / 39 × 100 = 56.4%.

The sequence is 56.4% GC and 43.6% AT.

These are the values the calculator opens with, so you can check its output against this example.

Assumptions

  • Only unambiguous bases are counted.
  • The whole sequence is treated as one window. Local GC content can differ widely along a long sequence.

Common mistakes

  • Reading GC content as a melting temperature. It is one input to Tm, alongside length, salt and concentration.
  • Pasting a sequence that still contains line numbers or annotation. They are stripped here, but check the reported length.
  • Comparing GC content between sequences of very different length without considering local variation.

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