Store sequence id in item data

Before the item map was only {sequence: data} and the data object did not
include the sequence attribute. I've fixed that so it now also includes the
sequence as part of it.
Check if we have 3D coordinates for all items

This will be useful later on when we have to display 3D coordinates. This way we
can prevent sending out bad requests and I can then remove logic dealing with
such things. In addition, it is easier to display to the user that there are no
3D coordinates for this base pair.
Update gitignore
Some things shouldn't be +x
Add place to mark if rows have no 3D

Not all things have 3D information associated with them. In these cases we will
mark the rows so people know this. This may not be the best way to this, but I
will use it for now.
More things to -x
Clean up my HTML a bit

Just change some spaces and add a missing action attribute for the form.
Reorganizing

I'm reorganizing the code so it is easier to update the displays. This involves
moving bits around to try and reduce the complexity and duplication.
Generate an id along with the pair and item data

It's useful to refer to a pair by id so we add one. In addition, we need to
refer to items by ids and I'm using something globally unique instead of just
unique to the family.