TFSearch Viewer is an easy to use software that submits multiple sequences to TFSEARCH server automatically, providing evidence for co-regulation of the set of genes via transcription factors at the transcription level.
The result file shows counts of each TFBS identified in each sequence, TFBSs are ranked by their occurence among all the sequences submitted, thus 100% ocurrence for a TFBS means the binding site can be detected in all the sequences.