The BAliBASE Reference alignment and query alignments by Clustal Omega and Praline of the sequence set BB30009.

<p>For the sake of visibility only core blocks of the MSAs and their flanking regions are shown in this figure. The core blocks in the reference alignment are highlighted in rainbow color scheme. The coloring scheme of the reference alignment are mapped directly onto the query alignments, so that shifts can be recognized easily. The MSA generated by Clustal Omega yielded an SP score of 0.48, shift score of 0.28, and SPdist a score of 0.59, while the MSA generated by Praline obtained an SP score of 0.46, shift score of 0.28, and SPdist a score of 0.78.