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...