Karoliina,
Here is a link to a trigger point chart I use for finding where knotted muscles are. I find it super useful, especially since the muscles causing the pain are not necessarily the muscles that have the pain. It will show you exactly where to massage for your specific problem. You may want to also look up "how to" massage the knots, because there are actually specific techniques. I have found that trigger points in my lower leg are some of the most painful I have ever worked out, so brace yourself.
http://www.triggerpointmaps.com/tp_finder.html
That's awesome, jldeleon! Thank you so much, that will sure come in handy!
I massaged and stretched both legs earlier today, and just came back from a run. No more pain, other than a little soreness from the massage. I'm so relieved it really doesn't seem to be a tendon overuse injury. Thank you everyone for your advice.