If one ignores these possibilities, one has distorted the data. Therefore, only one bit is needed to describe a position in a binding site that contains only purines, but two bits are needed to describe a position that always contains adenine. If the frequencies of bases are not exactly equi-probable, then a more sophisticated calculation is needed to find the average information at a position. The height of this curve is the height of the logo at that position. The bases are then stacked on top of each other in increasing order of their frequencies and plotted.
Vertical bars serve both as junction markers and as size markers.
When a binding site has two parts, it is possible to align both portions and create a logo for each. The spacing could be indicated by a histogram that shows the frequency distribution of the spacing. Alternatively, a logo could be created for each spacing. Since variable spacing reduces the overall information content of a pattern, the length of a downward pointing arrow could be used to indicate the amount of pattern reduction. In cases where there are few sequences, a meaningful logo cannot be made.