I'm sorry Thaman, but what do you mean by "alignment score? The number you see at the end (is that what you refer to as the "right column"?) is simply the number of AA from the start of that sequence...

The numbers on the right side of that file are sequence positions for each sequence, not scores, unless I am missing something.

Those aren't alignment scores, they're a counter for how far along the input sequence each break is. They are part of the Clustal format (The alignment score applies to the whole alignment, not one section of it).

Sorry i have misunderstood then, but output generated by the clustalw(.aln) doesn't have this record in the file. There are just sequence description and sequences in individual lines.

OK, I think you want to set the option -seqnos option to ON when you run clustal.

@David w- Thanks that's what i want.

Dear David, could you please enter your comment as an answer as well. That way people won't get discouraged when seeing an seemingly unanswered question.