First line is a comment line - default written by MULTALIGN is the filename. Subsequent lines are all free format position specific residue weights.
Eg.
> 1 (weights versus first posn. of block_file) a 3.0,g 4.0 p,2.0, (Alanine gly and pro given weights - others score 0) >2 (weights for second position of block file g 100, p 100, > 3 a 33, .. etc
See bash_day.look for a complete example. Note that if a residue is not defined at a position then its score at that position is zero.