The problem is caused by the order of the alignment. It seems likely that the order
is 1-2, 3-4, 6-7, 5-6/7, 1/2-3/4, and finally 1234 against 567. As 567 will be
aligned like:
5 ASDGRFGVCWPLKHTY 6 ASDFRFGVCWPLKHTY 7 ASDFGFGVCWPLKHTY ** |
and as there must be a gap, the insertion (-) will be placed such that the two Rs in 567 will align with the Rs in 1234, and the two Fs in 567 with the four Fs in 1234. The poor Gs in the columns indicated with the asterixes in the box, will both end up at a different position. The problem is that CLUSTAL treats the sequence 5, 6, and 7 as one sequence called 567 once they have been pairwise aligned early on in the process. Other alignment procedures use shake-and-bake like algorithms (i.e. randomly shake things around the gaps, and keep what you like best) to overcome these problems, but such algorithms are computationally very expensive.