Flowchart of CORE_TF runs. CORE_TF runs linearly through 6 web pages. Pages 1 and 2 take as input experimental gene/promoter lists and random gene/promoter lists or requests to create random lists. Depending on format, sequences are retrieved with Ensembl API or random lists generated before identifying TFBS with Match/TRANSFAC. A binomial test is run to identify over-represented TFBS in the experimental set compared to the random set and displayed in page 3 as a table. In the table TF and a promoter can be selected which are sent to page 4. If requested homologs and sequences or genomic alignments are retrieved from Ensembl for the selected promoter. If not already a genomic alignment input sequences or retrieved sequences are aligned with BLASTz. TFBS are identified with Match/TRANSFAC, overlapping TFBS are identified and scores calculated, and the data is displayed in page 5. Conserved TFBS can be selected and displayed as highlights in the alignment in page 6.