The parts were not 'in alignment'. = The parts were 'out of alignment'. [=the parts were not aligned]
Many people were surprised by his 'alignment' with the protesters. [=his support of the protesters]
The school has to bring its programs 'into alignment' with state requirements.
(..) It's possible you found one of these points. We are lucky that it remained open. Once the worlds pass out of alignment then the connection is lost. I like the way you explain things. What's going to happen to me? I'll find a way (..)2013 Thor: The Dark World
(..) From here, I can see nine realms and ten trillion souls. Do you recall what I taught you of the Convergence? Yes. The alignment of the worlds. It approaches, doesn't it? The universe hasn't seen this marvel since before my watch began. Few can sense it. (..)2013 Thor: The Dark World