Figure 1

A Mumsa alignment visualized by Kalignvu. A relaxed Mumsa alignment derived from a ClustalW, Poa, Kalign, Probcons and Dialign alignment of the Balibase 3.0 test case BB20007. The parameter f was chosen to be two, requiring that residues in the output alignment appear in at least two input alignments. Each residue is colored according to the average occurrence of the POARs it is involved in. Regions that appear in red are identically aligned in all 5 input alignments while green and blue regions are only aligned identically in fewer and fewer cases. It is clear that all alignment programs find conserved motifs in the sequences but disagree on how the residues in between should be aligned.