Motifs of interest were selected by applying a set of filters: specificity score [77] , quality of alignment (AlignACE MAP score) [97] , palindromicity [77] , and conservation. To determine the degree of conservation, a search matrix was constructed for each motif. Each of the other genomes was searched with this search matrix using CompareACE, and N-way conserved sites were identified. N-way conserved hits are hits identified upstream of orthologous genes in N genomes, where orthology is defined by membership in the same SYNERGY orthogroup. To select interesting motifs we required specificity score < 1e-10, palindromicity > 0.7, MAP score > 5, and at least 8 sites conserved in 8 genomes.