In discussion, another view about these repeats held that after an estimate of the repeat region was made, N's should be inserted, rather than making a force join. Annotation would otherwise be the same. GC-rich regions should be finished, not left as gaps. Under this view, representation of sized gaps by an appropriate number of Ns and submission of a gapped project as two separate submissions are not acceptable, and that gapped sequences should remain as phase 2. There is not universal agreement on this point, as some centers represent sized gaps by a string of Ns, while others force join contig ends and annotate.
Further discussion is warranted.
If at all possible the full sequence of the excised region should be given since insertion sequences can be polymorphic, although at present field size limitations preclude simply putting the sequence in a comment. The databases will need to help in deciding how to represent insertion sequences. Such annotations are optional and done at the discretion of the finisher.