GC Content Calculator

How it is calculated

GC content is the share of bases in a sequence that are guanine (G) or cytosine (C): GC % = (G + C) ÷ (A + T/U + G + C) × 100. The tool removes all whitespace, converts the sequence to upper case and counts the letters A, C, G and T or U, so both DNA and RNA work (U is counted with T). Any other character, such as N, digits, hyphens or FASTA header text, is ignored and does not count towards the length. It reports GC %, AT %, the number of valid bases and the G + C count. Only the whole sequence is analysed; there is no sliding window, so local GC-rich regions are averaged out.

Common mistakes

• Pasting a FASTA header line (starting with >) together with the sequence. The letters in the header name are counted if they happen to be A, C, G or T, which skews the result; paste only the bases.
• Expecting N or other ambiguity codes to count. Only A, C, G, T and U are counted, so unknown bases silently shorten the denominator.
• Treating the figure for a whole genome or long gene as if it applied to a short primer. GC content varies along a molecule and the whole-sequence average can hide local differences.
• Using GC % alone to predict melting temperature. It is only one factor; length and sequence order also matter.
• Entering a protein sequence. Amino acid letters such as A, C, G and T are also amino acids, so the tool would give a meaningless number.