Figure 1.

Profiling TA sites using the V_step algorithm. Sequences of 12 bp (N) with TA sites at positions six and seven were analyzed with respect to the 11 V_step values ([0]–[10]) for transitions from one base pair to the next (brackets). Profiles are charted and subsequently assigned to one of three categories, preferred, semi-preferred or basal, based upon the graphical pattern. In all profiles there is a ‘TA-peak’ that always exists in such profiles because the T-to-A V_step value is 6.3 and all steps from N to T and from A to N (N = any base) are always <3.0, as shown on the left side of the figure. The ‘TA peak’ formed by the two lines that connect the three V_step values for the N-to-T, T-to-A and A-to-N steps are shown in boldface.