A permutation analysis of all syntenic clusters that the Synteny Database found in the human genome using amphioxus as outgroup. We permuted the location of paralogous group members throughout the genome and reclustered the randomized data, repeating the randomization and cluster analysis 100 times for each window size. The mean number of clusters found for a particular cluster size are plotted with error bars. The number of clusters the Synteny Database found in actual human genome data is plotted with crosses.