Knee pulling

I have been experiencing some pulling feelings in my legs on the inside of my knees and I think that this could be due to a muslce imbalance. I went to a doctor and nothing 'wrong' was found with me. For 3 or 4 years I had been getting little physical activity as I was just sitting around all day and my muscles weakened.

It is hard for me to do the stretch that you see runners doing where they stand on one leg and pull the other leg back. I also can not sit indian style. I'm hoping that this info will help to figure out which muslce needs more strengthening or stretching. Any idea what my problem could be?
 
I should also add that I can do calf raises and squats fine. However, when I stand on one leg and raise the other leg backwards forming a 90 degree angle in my leg (after a few times) it causes the pulling feeling. I get the same feeling if I sit in a chair feet flat on the floor and then raise one leg up off of the ground without bending my leg.
 
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