Promoter Heterozygosity and Function

We use nucleotide diversity ($\pi$), or the average number of nucleotide differences per site between DNA sequences. Using 500+ inbred lines of D. Melanogaster, we calculated the nucleotide diversity around a neighborhood of $\pm$200 bases from Transcriptrion Start Sites (TSS). Initial results show much higher diversity around TSSs when compared to exons and introns. We are currently searching for patterns of nucleotide diversity among types of promoters as well as among different organisms.