In order to align sequences i use Clone Manager, however, when I try to align 4 or more sequences, I do have problems with the alignment...Some of the sequences which should align 100% with the sequence of interest does not show 100% complementarity ….If I align only 3 of those sequences…the problem disappear. Can someone give me a tip or advices how to solve this problem?

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P.S I hope, i was to some extend clear with the description

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