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.