I want to know if animation can be done over video or not. It is easy in After Effects, you just import videos and can do animations. How can I do this if I am doing this in Synfig?
See the example
It’s possible: You just import the video and animate over it. 
File->Import / Ctrl+I -> Select Video -> click import -> animate -> export -> profit
Just keep in mind that Synfig is not a video editor and thus should not be expected to behave as such.
That’s why you import the video frames in Synfig as background/blueprints (canvas size = frame size).
Your video is still the reference for timing.
But when you will do the final mix, just export your animation as PNG with transparency or maybe H.264 lossless.
And mix the final result in a non-linear video editor like KDEnlive
@BobSynfig but then I have to select each image to import as only one thing can be imported in Synfig. Is there any way to import in image sequence? Sorry If I am not able to understand you.
There is File->‘Import Sequence’ for that.
Also make sure your animation framerate is equal to what the movie has you want to animate over
You’re right, my bad for assuming you were using the latest version.
An old way of importing an image sequence is described here: https://wiki.synfig.org/Doc:ListImporter
Maybe this can solve your issue