The parameter settings are: Searching only forward strand; K=3; motif width between 8 and 20; module length fixed as 100 for simulation 1 and 200 for simulation 2. For simulated data, the locations and seqeunces for generated motif sites for each dataset are also included. 1) Simulation 1: **site1.txt -->(YY1), **site2.txt -->(c_MYC), **site3.txt -->(E2F). 2) simulation 2: **site1.txt -->(E2F), **site2.txt -->(YY1), **site3.txt -->(c_MYC).