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Degenerate primers
A degenerate primer is a mixture of otherwise identical primers where one or more of the positions can have multiple alternative bases. These degenerate bases are represented by specific letters, each denoting one type of variation. For example, a letter B in the primer sequence means that some primers in the mixture can have C in that position, while others can have G or T (see the table below).
The following letters are used to designate degenerate bases in a primer sequence:
| B | D | H | K | M | N | R | S | V | W | Y |
C/G/T |
A/G/T | A/C/T | G/T | A/C | A/C/G/T | A/G | G/C | A/C/G | A/T | C/T |
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