Both A477T and GRα occupy ‘half site’ GBRs in vivo . Motif analysis was performed using MEME-ChIP on three groups of GBRs (results shown by row): occupied by GRα only (top row), occupied by both GRα and A477T with ≤1.4-fold difference (second row), and occupied by A477T only (third row). GR motifs (left column) from GBRs occupied by GRα only are similar to the canonical full site. In contrast, GR motifs from GBRs occupied by A477T only consist of a ‘half site’ motif, which lack the second adjacent half site. GR motifs from GBRs occupied by both GRα and A477T contain a very weak second half site, separated by the normal three bp spacer. GR motifs were forced to 17 bp in all samples, but an unbiased search revealed shorter 11 bp motifs at GBRs occupied by GRα and A477T, or A477T alone (Additional file 10). GR motifs are centrally enriched in all samples (P < <0.01). Motifs that were similar to those for STAT (center column) and AP1 (right column) family transcription factors were also found, although the AP1 motif was not enriched at GBRs occupied by only A477T. The bottom row shows the JASPAR motifs for STAT3 (MA0144.1) and AP1 (MA0099.2) as a reference, and the vertical dashed lines indicate their alignment with discovered motifs.