ok, so my problem is that i was making this object and when i tried to duplicate special with instance on -y scale just so that i get an exact similar flipped instance on y axis , then i noticed this box gizmo was rotated when i pressed ctrl + t . i want to align it with my object by rotating it , how do i do that ?
Activate the move tool (w) and edit its pivot...then do a Modify->Bake Pivot. Now when you activate the universal manipulator, it should show up in the new position.
You can edit pivots manually.
The hotkey is insert.
http://help.autodesk.com/view/MAYAUL/2016/ENU/?guid=GUID-150B390E-840B-4FE3-B8E9-8DEBCE7CEC97