View→Overview window
Select the overview window menu item to get a navigable image of the whole alignment.
The red box indicates the currently viewed region of the alignment, this may be moved by clicking and dragging with the mouse.
Right-click (or CMD-Click) to open the
overview's popup menu. This provides an option to include hidden
regions in the overview (shown as dark-grey rows and columns).
The option to include/exclude hidden regions in the
overview was introduced in Jalview 2.10.2.