Successive steps of the dynamic programming scheme for a Greek key motif 5436, σ = 1 2 5 4 3 6. Arrows show the "waiting" constraints. As all the (loop or adjacency) constraints have not been satisfied by determining the linked segments, a segment should be considered as a variable with the memory of a partial solution for each possible instance. The corresponding ranks are said "active" and are listed in the conf set.
Tran et al. BMC Genomics 2012 13(Suppl 2):S5 doi:10.1186/1471-2164-13-S2-S5