What are the meanings of the three symbols “*”, “.”, and “:” in ClustalW?

Last updated:2015.6.8.

These symbols are used to indicate amino acids aligned at the sites marked with the symbol.
“*” indicates perfect alignment.
“:” indicates a site belonging to group exhibiting strong similarity.
“.” indicates a site belonging to a group exhibiting weak similarity.
The criterion for distinguishing strong from weak similarity is as follows: Strong similarity corresponds to a PAM250 MATRIX score between amino acids of greater than 0.5, while weak similarity corresponds to a score of 0.5 or less. In the README excerpt, the lines horizontally adjacent to the phrases
     STA
     NEQK
     :
indicate the amino-acid groups in cases for which the corresponding symbol is present (These are written using single-character notation for amino acids).

The README file included with the ClustalW source package contains the following text.
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12. The conservation line output in the clustal format alignment file has been changed.
Three characters are now used:
'*' indicates positions which have a single, fully conserved residue
':' indicates that one of the following 'strong' groups is fully conserved:-
       STA       NEQK
       NHQK
       NDEQ
       QHRK
       MILV
       MILF
       HY
       FYW
'.' indicates that one of the following 'weaker' groups is fully conserved:-
       CSA
       ATV
       SAG
       STNK
       STPA
       SGND
       SNDEQK
       NDEQHK
       NEQHRK
       FVLIM
       HFY
These are all the positively scoring groups that occur in the Gonnet Pam250
matrix. The strong and weak groups are defined as strong score >0.5 and weak
score =<0.5 respectively.
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