Segregating sites are positions which show differences (polymorphisms) between related genes in a sequence alignment (are not conserved). Segregating sites include conservative, semi-conservative and non-conservative mutations. The proportion of segregating sites within a gene is an important statistic in population genetics since it can be used to estimate mutation rate assuming no selection. For example, it is used to calculate the Tajima's D neutral evolution statistic.
See also
Conserved sequence Ultra-conserved element Sequence alignment Sequence alignment software ClustalW
References