Answer:


S1               CWPAASTFLGAACPW
S2               CWPASSN--GSACPW

S1               CWPAASTFLGAACPW
S3               CWPRASTN-AAACPW
S2               CWP-ASSN-GSACPW

S3               CWPRAST-NAAACPW
S4               CWPRASSYNAAACPW
S1               CWPAASTFLGAACPW
S2               CWPASSN--GSACPW

S2               CWPASS--NGSACPW
S5               CWPASSTFNGAACPW
S1               CWPAASTFLGAACPW
S3               CWPRAST-NAAACPW
S4               CWPRASSYNAAACPW

Each time, after adding 1 sequence you feel that you are looking at the best possible alignment, and still, eacht time things are different from how they were before. That is because you are doing the same as a good multiple sequence alignment program should do, you use all information at the same time. You see each time which residues are most conserved and thus should lign up. In practice, this does not always go so well. All problems seen in previous exerciese can always pop up. Believe me, making this exercise behave like a perfect world example wasn't easy...