If you're using https:
rather than git:
for your clone, it's possible that it's barfing on the CA certificate, i.e. you don't have a copy of the intermediate certificate to verify your SSL connection. I've run into this on a couple of different occasions. Usually with debian-based Linux distributions. Try
git config --global http.sslVerify false
and then the clone again. If the clone works, that's what's happening. However this is a bad solution, as of course turns off SSL verification, which makes using HTTPS somewhat pointless, and leaves you vulnerable to man-in-the-middle attacks.
What you need to do is download the CA Certificates package for whatever OS you're on, under Linux (well Debian/Ubuntu) it'll probably be something like
apt-get install ca-certificates
then
git config --global http.sslVerify true
git config --global http.sslCAinfo /etc/ssl/certs/ca-certificates.crt
although your path to your certificate file might be different depending on OS version.
This should get it working.