e115 Nucleic Acids Research, 2005, Vol. 33, No. 13 location of peaks is shifted towards smaller base counts for A and T, and towards higher counts for C and G when compared to bacteria and archaea. The Z-values are very high for the eukaryotic organisms. Valid and redundant oligonucleotides The distribution of the unique, valid and redundant oligonuc- leotides within the genes and ﬂanking regions were estimated by calculating Z-values. The ﬂanking regions of eukaryotic genes are numbered as 0 and 8 in Figure 5A, where coding regions have been divided into seven equal partitions. If there was uneven number of nucleotides, the middlemost (4th) partition was shorter. Both the 50 and 30 ﬂanking sequences are highly underrepresented among the valid oligonucleotides. The reason is that these regions contain common and therefore conserved patterns involved in transcription and translation start and stop. In all these genomes, the last section contains slightly reduced proportion of valid oligos. The bacterial and arhaeal genomes have quite unbiased distribution throughout the genes. It has been a general trend to select probes, for C PAGE 10 OF 16 example for antisense and microarray applications from the beginning of genes. The ﬁrst and last sections in eukaryal genomes are somewhat surprisingly overrepresented among the unique and valid oligos. As a conclusion, oligonucleotides can be selected almost equally well from all the sections within coding region whereas in eukaryotes the ﬂanking regions contain much less than expected of valid and unique oligonucleotides. When looking at the ratio of the valid and invalid oligos (Figure 5C and D), the same trends are apparent. In all the organisms, the graphs have remarkably ﬂat distribution except for sections 0 and 8. The section 7 is universally some- what decreased in all the prokaryal genomes. Sections 1 and 7 contain only slightly higher ratios than sections 2–6 for eukaryotes. Effects on codon usage The effect on the coding properties of the valid oligonucleo- tides was studied by calculating the Z-values for the distribu- tion of each codon (Figure 6). The expected codon frequencies