Figure 2 and 3 show four of the seven Hox clusters of the pufferfish Takifugu rubripes. Despite the fact that the Hox genes within a paralogy group are significantly more similar to each other than to members of other paralogy groups, there are several features that make this dataset particularly difficult and tend to mislead automatic alignment procedures: (1) Neither one of the 13 Hox paralogy groups nor the Evx gene is present in all four sequences. (2) Two genes, HoxC8a and HoxA2a are present in only a single sequence. (3) The clusters have different sizes and numbers of genes (33481 nt to 125385 nt, 4 to 10 genes).