problems with 2001 ford focus?

I have problems with my 2001 ford focus. When I was driving at a speed of 35-45mph it seemed my car is coughing.. and struggling. I don't think its the transmission since it doesn't seem it is switching gears when I notice the problem. I have just put fuel/engine cleaner in my gas tank today and haven't driven that much yet. It seems to be getting progressively worse not only limiting the problem to the 35-45 speed. I just had a full tune up, oil change changed the air filter so now I am stumped. Any suggestions?
 
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