Yes, it does - at the very least, the header will have name and GenBank ID (and IPD ID, when available). If there's anything else that would be easiest to add via the header like that (any of our region, locus, species, origin info, etc.) I could easily build those into the header as well. Basically, as long as I know what info needs to be in the header I can make sure that it's there.
Also, would it be possible to change over the current "full length" check box to a drop down of "full length", "partial", and "short"?