Identifying putative TF binding sites using a DNA motif. (A) A DNA motif for TF Gcn4 is used to identify putative Gcn4 binding sites, defined as sites with LLR score > F × the LLR score of the best DNA site according the motif (here, ATGAGTCAT). (B) Putative Gcn4 binding sites reported by JASPAR (Mathelier et al. 2014) using the Gcn4 motif MA0303.1 and a relative score cutoff F = 0.8.