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Here is the default layout of the editor:

<center>
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     <img src="/wiki/download/attachments/4227444/Alignment Editor Components.png"/>
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</center>

The Alignment Editor components:

For example, let’s assume that the coordinate of the first visible base of the row is N, but the row contains K gaps before the position N. The starting offset value will be N-K. The same rule is true for the ending offset.

You can turn off the Sequence offsets by unchecking the Actions ‣ View ‣ Show offsets main menu item or View ‣ Show offsets context menu item.