Potential retinoic acid and thyroid hormone receptor binding sites conserved in AluSx of NWMs. The nucleotide sequence (1–89) of the AluSx of each primate was aligned with the consensus AluSx sequence. The location of four direct repeats is indicated within each box with the consensus sequence indicated below each. The potential retinoic acid receptor binding sites (DR2) and the thyroid hormone binding site (DR4) are indicated above the boxes. The locations of the A- and B-boxes of the Alu are indicated below the sequences. The G-to-A and C-to-A change in positions three and five in the third direct repeat occurs in the human, all apes and OWMs, but not NWMs. These changes would likely abrogate binding of TR and RAR to the DR4 and the second DR2, respectively. All NWMs acquired a G-to-A change in the sixth position of the fourth direct repeat thus creating a potentially better DR2 for retinoic acid receptor binding. The third direct repeat in NWMs was unchanged from the consensus Alu sequence and would provide an ideal direct repeat providing a potentially functional DR4 and DR2.