Dubbed "Tom's T" by Dhruba Chattoraj, the unusually conserved thymine at position +7 in bacteriophage P1 plasmid RepA DNA binding sites rises above repressor and acceptor sequence logos. The T appears to represent base flipping prior to helix opening in this DNA replication initation protein.
Schneider.baseflip.2001 T. D. Schneider. Nucleic Acids Res. 29:4881-4891, 2001.