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Clustal was the first aligner that handled multiple sequences, i.e. that went beyond pair-wise alignment.

File format

The alignment is columnised into characters of 60 so that the alignment is spread over several rows separated by blank lines. Below the rows of aligned characters there is an extra "cons" row which is qualitative conservation indicator. It is a space character if there is a mismatch, a period character if the site can be caleld semi-conserved, a colon if can be called conserved, and finally an asterisk if there is a complete match.