Repeating orderings incorrectly represented in sort menu.

When alignment orderings repeat for different regions the entries in the sort menu show incorrect region numbers. E.g if orderings are A|A|A|A|B then the sort menu entries are "Region 0,1,1,1 Ordering" and "Region 1 Ordering" while they should be "Region 1,2,3,4 Ordering" and "Region 5 Ordering"
The issue is caused by changing item indexes while iterating over the array in ``MsaWSThread#addSortByMenuItems``. A quick fix would be to iterate over the array backwards and then reverse the order of the results. This, however, might not be fully sufficient for partially completed jobs.