Test for clustered pentamers or hexamers. The light blue lines at thetop represents the position of the sequence element along all upstream regions in a given data set—in this case, late G1. The scale for these blue lines is along the right axis; the scale for all other lines is along the left axis. The pink histogram is a cumulative representation of the light blue lines, i.e., it shows the (normalized) cumulative number of oligomers present at that position. The dark pink line is the expected (normalized) cumulative number of sequence elements at that position, if the element is not clustered along the upstream region. Both elements ACGCGT and CGACGC are over-represented in late G1 (Table 1). The two overlapping pentamers that make up ACGCGT, ACGCG, and CGCGT are both over-represented in late G1 in the interval from −104 to −202 nucleotides upstream of the ATG start codon (Table 2). One of the two pentamers that makes up CGACGC, GACGC, is also over-represented in late G1 in the interval from −104 to −202 nucleotides upstream of the ATG start codon (Table 2). However, although the 87 ACGCGT hexamers are clustered along late G1upstream regions according to the statistic used here, the 41 CGACGC hexamers are not clustered. Empirically, the ACGCGT hexamers are clustered between ∼−100 and −200 nucleotides upstream of the ATG start codon.
