IUPAC Nucleotide Codes — Full Ambiguity Code Table
The IUPAC nucleotide codes are single letters that stand for a set of possible bases, so an ambiguous position can be written as one character. The four bases keep their letters (A, C, G, T / U), and eleven extra codes (R, Y, S, W, K, M, B, D, H, V, N) cover every other combination. This is the full table with the bases each code matches, its mnemonic and its complement.
| Code | Matches | Mnemonic / meaning | Group | Complement |
|---|---|---|---|---|
| A | A | Adenine | Base | T |
| C | C | Cytosine | Base | G |
| G | G | Guanine | Base | C |
| T | T | Thymine | Base | A |
| U | U | Uracil (RNA) | Base | A |
| R | A, G | puRine | Two bases | Y |
| Y | C, T | pYrimidine | Two bases | R |
| S | G, C | Strong (3 H-bonds) | Two bases | S |
| W | A, T | Weak (2 H-bonds) | Two bases | W |
| K | G, T | Keto | Two bases | M |
| M | A, C | aMino | Two bases | K |
| B | C, G, T | not A (B follows A) | Three bases | V |
| D | A, G, T | not C (D follows C) | Three bases | H |
| H | A, C, T | not G (H follows G) | Three bases | D |
| V | A, C, G | not T/U (V follows U) | Three bases | B |
| N | A, C, G, T | aNy base | Any | N |
How to read the codes
The two-base codes pair up by chemistry: R/Y split purines from pyrimidines, S/W split strong (three hydrogen bonds) from weak (two) base pairs, and K/M split keto from amino. The three-base codes are named for the base they exclude — B, D, H, Vare the letters following A, C, G and U in the alphabet, each meaning “not” that base. N matches anything.
Frequently asked questions
- What does N mean in a DNA sequence?
- N is the IUPAC code for any base — A, C, G or T. It is used where the base is unknown or could be any of the four, for example in degenerate primers or low-confidence sequencing positions.
- What does R mean in DNA?
- R stands for a puRine — either A or G. Its complement is Y (a pyrimidine, C or T).
- What is the complement of an IUPAC ambiguity code?
- Complement each code to the code representing the complementary base set: R↔Y, K↔M, B↔V, D↔H, while S, W and N are their own complements. For example the complement of R (A/G) is Y (T/C).
- Why are degenerate bases used?
- They compactly represent a position that can be more than one base — essential for designing degenerate primers, describing motifs and recording ambiguity in consensus sequences without writing out every possibility.