Actually when I tried to clone it was also giving the error in alert box that
The server's host key is not cached in the registry
with option yes or no then I selected Yes then it gave me the error
unable to open connection. Host does not exist
So the solution is saving the host key in registry
Open up cmd and go to path of plink (mine was C:\Program Files (x86)\GitExtensions\PuTTY) and type plink user@whateveryourserver.com
This will prompt you to save the host key in registry , and enter yes, then try your git command again, and it should be working.