As an example, Figure 4 shows an alignment calculated by the non-anchored default version of DIALIGN for BAliBASE reference set lr69. This sequence set consists of four DNA-binding proteins and is a challenging alignment example as there is only weak similarity at the primary sequence level. These proteins contain three core blocks for which a reliable multi-alignment is known based on 3D-structure information. As shown in Figure 4, most of the core blocks are misaligned by DIALIGN because of the low level of sequence similarity. With the BAliBASE scoring system for multiple alignments, the default alignment produced by DIALIGN has a sum-of-pairs score of only 33%, i.e. 33% of the amino-acid pairs in the core blocks are correctly aligned. The column score of this alignment 0%, i.e. there is not a single column of the core blocks correctly aligned.