Figure 2

Information content and differences in the context between two sites of Gallus gallus. The nucleotide sequences were selected for the determination of nucleotide frequency at positions between -15 and +15 (codon AUG corresponds to position +1 to +3). The application of two different ways of displaying the consensus sequences allows one to display the nucleotide periodic frequencies in addition to the site information content. In the analysis performed a consensus context was deduced as a"............(G/A).(C/G)ATG G.............." and "...........(G/C)..(G/C)ATG..............." for first and second in-frame downstream AUG, respectively. The total information content consisted of 9.6 and 6.6 bits for these sites. (A) First AUG site (n = 3135). (B) Second in-frame downstream AUG site (n = 1190). The frequency of each consensus base is indicated on the left Y axis, according to the 50/75 consensus rule. On the right Y axis, the lines represent the degree of site conservation measured in bits of information according to the equation given in the methods section. The continuous line is the information content without correction, and the broken line is the same information corrected for bias.