Schematic drawing of the model structure. The triangle and rectangle represent the first and second motif respectively. Gray boxes indicate valid locations for the second motif given the position of the first. The "phase" (distance offset) is assumed to be constant over all sequences and is determined by the algorithm.
Larsson et al. BMC Bioinformatics 2007 8:418 doi:10.1186/1471-2105-8-418