Are you saying you have (are given) the pairwise alignments (as strings with dashes) and all you need to produce is the "Final Multiple sequence alignment"?

Also, it there a typo? 

............V
Ref1: CGACAAT--GCACGACAGAGGAAGCAGAACAGATATTTAGATTGCCTCTCATTTTCTCTCCC
Seq1: CGACAAAAAGCACGACAGAGGAAGCAGAACAGATA-----ATTGCCTCTCATTTTC-CTCCC
............^

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In reply to Re^3: how to construct multiple sequence alignment from group of pairwise alignments by BrowserUk
in thread how to construct multiple sequence alignment from group of pairwise alignments by gudluck

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