The character "." has to be used as a gap character, since empty cells signal the end of a sequence or alignment. To replace other gap characters placed by an extrernal alignment program or to fill empty cells placed during manual gapping, run the macro "AA_Empty" over the sequence alignment.

Check again:

• The first row contains the chain label, "L" for antibody light chains, "H" for heavy chains, "A" for TCR alpha chains, and so on.
• The second row contains the residue label
• The third row contains the insertion code, if needed
• The alignment starts in row four
• Gaps are indicated by "."
• The sequences are in the same order as they were at the beginning

If everything looks OK, you are ready to continue