Differences among TFB motifs among sequence data sets. A multiple alignment of significant matches to the TFB motif from each data set reveals the general BRE-TATAbox-PPE-TTS layout for all data set. The putative BRE, TATA box, PPE, and TSS in the logo are indicated with colored rectangles (red and green, BRE; white, TATA box; PPE, black; TSS, vertical white), and text annotation. Differentially emphasized elements within the BRE may confer specificity for binding of one or more TFB proteins. Specifically, an emphasized ‘AA’ 4 bp upstream of the TATA box was discovered in all datasets that contain sites that bind TfbG (turquoise box, TfbG, TfbBG, TfbDG, and TfbBDG), and ‘CG’ 7bp upstream of the TATA box was emphasized most for sites that can bind both TfbB and TfbD (full red box, TfbBD and TfbBDG data sets), intermediately for sites that can bind either TfbB or TfbD but not both (half red box, TfbB, TfbD, TfbBG, TfbDG data sets) and least for sites that can bind neither TfbB nor TfbD (TfbG). The similarities and differences discovered within the BRE invite future experimental investigations.