Ambiguous nucleotide

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Ambiguous nucleotides are used when the true nucleotide is unknown. The most popular one seen with high-throughput genome sequences is "N" which represents any possible nucleotide.


  • N Any nucleotide (A or C or G or T or U)
  • R Purine (A or G)
  • Y Pyrimidine (T or C)
  • K Keto (G or T)
  • M Amino (A or C)
  • S Strong interaction (3 H bonds) (G or C)
  • W Weak interaction (2 H bonds) (A or T)
  • B Not A (C or G or T)
  • D Not C (A or G or T)
  • H Not G (A or C or T)
  • V Not T or U (A or C or G)

Not ambiguous

  • A Adenosine
  • C Cytidine
  • G Guanine
  • T Thymidine
  • U Uridine (if 'Alphabet' set to 'RNA')