To find out which component of DIALIGN is to blame for its unsatisfactory performance on some of the BAliBASE data, we applied our program to BAliBASE (a) using the non-anchored default version of the program and (b) using the core blocks as anchor points in order to enforce biologically correct alignments of the sequences. We then compared the numerical DIALIGN scores of the anchored alignments to the non-anchored default alignments. The results of these program runs are summarised in Table 3. The numerical alignment scores of the (biologically correct) anchored alignments turned out to be slightly below the scores of the non-anchored default alignments.