The present version of the model server will in this case leave a gap in the model structure. In the near future we will add some software to automatically close the gap if this can be done in a straightforward manner. Here the only correct answer is everything. The error we have seen most often sofar is that people produce sequence files with MSword or a similar text editor. The server has no means of dealing with this problem.
Some people call it a bug in the program if there is a gap in the structure to be modelled.
However, if the alignment is wrong, a deletion will and up at the wrong spot, and a big gap will be the result. Insertions are not yet modelled. In the future we will also model short insertions, but presently we are lacking the CPU power to provide this service, and there are no good algorithms on the market that reliably build insertions. Another nice error to make is to put the model sequence all on one line that is longer than 80 characters. The characters beyond position 80 are NOT read, and only WHAT IF knows what the resulting model will look like.