Hand-Mixed Bases, also known as degenerate, random, or wobble bases, can be introduced at any position in an oligonucleotide sequence. When using the Oligo Entry Tool , use the Mixed Bases tab to select your desired IUB symbol and the percentage of each base. A table for mixed base notation is shown below.
For the first occurrence of a particular mixed base, the proportion of each base must be indicated, in the order ACGT. For example, an N mixed base that requires 25% of each included base will be indicated as (N:25252525); if the bases are required in the proportions 26% of A and T, and 24% of C and G, the mixed base will be represented as (N:26242426). Each mixed base after the first insertion of that ratio will not need the ratio, just the base in parentheses, e.g. (N).
Multiple mixes are possible, for a total of 4 maximum per oligo.
See example sequences below:
Example 1: ACGSSSACT with 50% of C and G for all of the S bases would be indicated as follows: ACG(S:00505000)(S)(S)ACT
Example 2: ACTGACTGNNNNNNNNNACTGATGC with 25% of A, C, G, and T for all of the N bases would be indicated as follows: ACTGACTG(N:25252525)(N)(N)(N)(N)(N)(N)(N)(N)ACTGATGC
Example 3: ACTGACTGNNNNNNNNNNCAGTACTG with the first 5 N-bases being equimolar, and the latter 5 N-bases being a 70/10/10/10 mix (favoring A): ACTGACTG(N1:25252525)(N1)(N1)(N1)(N1)(N2:70101010)(N2)(N2)(N2)(N2)CAGTACTG
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