Table 2 Aligned sequence positions that result from fragment aligments in the Fugu Hox cluster example. To compare these alignments, we counted the number of columns where two, three or four residues are aligned, respectively. Here, we counted only upper-case residues in the DIALIGN output since lower-case residues are not considered to be aligned by DIALIGN. The number of columns in which two or three residues are aligned increases when more anchors are used, while the number of columns in which all sequences are aligned decreases. This is because in our example no single Hox gene is contained in all four input sequences, see Figure 2. Therefore a biologically correct alignment of these sequences should not contain columns with four residues. CPU times are measured on a PC with two Intel Xeon 2.4GHz processors and 1 Gbyte of RAM.