We investigated not only the biological quality of the anchored and non-anchored alignments but also looked at their numerical scores. Note that in DIALIGN, the score of an alignment is defined as the sum of weight scores of the fragments it is composed of [17]. For some sequence sets we found that the score of the anchored alignment was above the non-anchored alignment while for other sequences, the non-anchored score exceeded the anchored one. For example, with the sequence set shown in Figure 2, the alignment score of the – biologically more meaningful – anchored alignment was > 13% below the non-anchored alignment (see Table 1). In contrast, another sequence set with five HoxA cluster sequences (TrAa, TnAa, DrAb, TrAb, TnAb) from three teleost fishes (Takifugu rubripes, Tr; Tetraodon nigroviridis, Tn; Danio rerio, Dr) yields an anchored alignment score that is some 15% above the non-anchored score.