I was recently treated for and cleared of chlamydia I

Patient : I was recently treated for and cleared of chlamydia. I was prescribed a 10 day (2 pills a day) supply of doxycycline, returned to the Dr. about a week after finishing my medication for a follow up test and results came back negative. My testicles/groin area are still a little sore/tender, and I'm afraid I may have epididymitis, though I did read that the tenderness can take a few weeks to disappear. I don't have any other symptoms other than soreness/tenderness in the groin area, which seems to be concentrated around my right testicle (which is larger than my left, I never noticed this before but I believe this is a normal thing?). My question to this issue is two fold: would the basic urine samples my doctor took to test for chlamydia detect epididymitis? If not, would the doxycycline treat it as well?
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