The results obviously depend on the divergence of the proteins, the number of sequences, the length of the motifs and the indel penalties but were often disappointing. Note that these motifs should be highly conserved and retain the most information enabling a correct alignment. ClustalV was one of the better algorithms but would still often miss these motifs. When all is said and done, people will still find that the alignments produced by the programs can be improved by a judicious and critical examination by eye. Spending time to slowly and carefully examine your alignments by hand is recommended.
Many algorithms make some use of a tree or phylogeny in the construction of the alignment.
It is how this information is used that can create some of these problems. This will incur the same penalty in the local alignment whether it is placed to the left or to the right. Yet all biologists recognize that this is not the case. We also have little idea of what appropriate penalties are. As a result, the alignments can always be improved by a careful examination.