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

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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