Fluorescent markers are used to sequence the DNA. The markers (shown top) consist of a series of 10 bases that bind to the portion of DNA to be sequenced (light green, lower image). Nine of these bases are universal bases (shown as gray), meaning that they can bind anywhere on a piece of DNA. The tenth base is one of the four DNA letters, C, A, T, and G, which can only bind to their corresponding base.

A total of 40 different markers are used, in 10 groups of four. In the first group, each lettered base would be in the first position, with each of the four types of markers labeled with a different color. In successive groups of four, the position of the lettered base moves down the sequence until there are enough markers to represent each DNA letter at every position on the 10 bases. (Shown here is the case in which the lettered base is in the fourth position.)