An overview of the operation of CoReg. The expression data output from ModuleFinder is taken as input (A) and the user defines the number of groups for analysis by CoReg. Files are also saved for visualization of expression data by MAPMAN. B) Sequence elements are identified that are unevenly distributed between the promoters of groups defined in A. The frequencies of these elements in each group are recorded. C) Various combinations of elements can be selected and saved.