Ovarian cyst or ovulation?

Miranda
My stomach has been hurting off and on for about a week and I've been spotting since I've ended my period. I just started my fertile week and just got off the xulane patch. It's either in the middle of my lower stomach or towards the right. I've been to the doctor for other symptoms related to a thyroid problem and she said if my stomach doesn't feel any better she may consider doing an ultrasound. She did a pregancy test and it was negative. Is it just ovulation or do I have a cyst or my appendix or what?