.aln

Source

ALN/ClustalW2 format was originated in the alignment program ClustalW2. It is a plain text file. The file starts with word "CLUSTAL" and then some information about which clustal program was run and the version of clustal used. e.g. "CLUSTAL W (2.1) multiple sequence alignment" The type of clustal program is "W" and the version is 2.1.

The alignment is written in blocks of 60 residues. Every block starts with the sequence names, obtained from the input sequence, and a count of the total number of residues is shown at the end of the line. The information about which residues match is shown below each block of residues:

   "*" means that the residues or nucleotides in that column are identical in all sequences in the alignment.
   ":" means that conserved substitutions have been observed.
   "." means that semi-conserved substitutions are observed.

An example is shown below.

   CLUSTAL W 2.1 multiple sequence alignment
   
   FOSB_MOUSE      ITTSQDLQWLVQPTLISSMAQSQGQPLASQPPAVDPYDMPGTSYSTPGLSAYSTGGASGS 60
   FOSB_HUMAN      ITTSQDLQWLVQPTLISSMAQSQGQPLASQPPVVDPYDMPGTSYSTPGMSGYSSGGASGS 60
                   ********************************.***************:*.**:******