Hi,
Welcome to the forum. I am really pleased to help you out. Pregnancy definitely is the first thing which needs to be ruled out in view of your symptoms and especially because you had sexual intercourse during the unsafe period. I would suggest you to get your serum HCG levels estimated since this is more specific than urine for pregnancy tests & it gets elevated in blood much early (around 10 days after the implantation of the zygote, formed by the union of an egg and a sperm).
The urine pregnancy test is usually done around 1 week after the missed periods. The HCG (it is a hormone) levels rise only in pregnancy and its presence will confirm the status of your pregnancy. If the pregnancy test is negative, then other causes of your symptoms needs to be looked into. Please do consult a gynecologist for the same. I sincerely hope that helps. Take care.