runner here! I have probably experience just about every running related injury known to man
It sounds like runners knee to me, but never fear, it isn't that serious. A little RICE treatment and you should be fine. But please, get thee to a store and get a new pair of shoes. There is NOTHING worse for your joints than running in a pair of worn down shoes. Try to keep track of your mileage and get a new pair every 200 to 300 miles (this depends heavily on your weight... the lighter you are, usually your shoes will last a little longer). And do me a favor and find a specialty running store. Bring your old shoes with you; they will be able to fit you with a shoe based on your size, stride, wear patterns, etc.
Last but not least, STRETCH, STRETCH, STRETCH! I have the same problem with tight muscles, and if I even skip one day of stretching after a long run or bike ride, I know I'm asking for trouble. Really focus on those hamstrings... and it might be a good idea to get a sports massage to help loosen them up on occasion. Hope this helps!
Happy running

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