File format of substitution matrix in clustalw
This example seems to have information on this, looks like it should have this format:
   A   G   C   T   U   *
A  1   -1  -1  -1  -1  -1
G  -1  1   -1  -1  -1  -1
C  -1  -1  1   -1  -1  -1
T  -1  -1  -1  1   -1  -1
U  -1  -1  -1  -1  1   -1
*  -1  -1  -1  -1  -1  -1

However, the page I linked is specifically about a bug regarding ClustalW ignoring custom made matrices. It's a pretty old post so it might have been fixed since. However, if you encounter that bug, that same page thankfully does contain a workaround!