SCANPS can output more than one alternative alignment for each sequence in the score list. You turn this option on by adding:
-top_only 0to the command line. The output in the file test_200_probcut30_toponly0.log is an example of output produced with this command. The test.fa query is an Annexin domain, and many Annexins contain multiple copies of this domain. SCANPS finds these and outputs them both as pairwise alignements, and as the multiple alignment.
KNOWN BUG - July 2002: If you set -top_only 1, you should only see one alignment per pair of sequences. However, some sequence pairs will show more than one. This is a known bug and will get fixed in due course.