Alignments as partitions of the set of sites (end). Toy example (end) - The alignment of the same sequences as produced by DIALIGN 2 with the featured partial columns included as anchor points. Almost all MS4 partial columns are now part of the alignment, except T1-3. The set of MS4 partial columns for this example is consistent, as can be seen by simply sliding the lowest occurrence of T1-3 below its corresponding fellow. The perturbation in the alignment is however sufficiently penalized by the optimisation function of DIALIGN to be rejected from the final alignment.