What Causes Soreness And Black Marks On The Penis After Intercourse?

I notice that my penis was sore a few hours after having unprotected sex..It hurt when it's touched or brush against my clothes..I went to the hosipalt and was test for Chlamydia and Gonorrhea .They also did a urina analysis, all of which came back negative..It feel like its a cut and Im starting to notice black marks..Similar to a scab..Any Ideas?