Late Periods. A reply at the earliest.

Hi Doctor I had protected sex with my girlfriend on 21st(20/03/2017) and 22nd(21/03/2017) day after her periods. She is 22 years old now and having hypothyroidism(for which she is taking 25mg tablet). She gained weight after her last periods. Her periods was due on 27th of this month(Usually get regular periods, except a couple of times). Its 31st now, 5 days late. Took HCG urine test both on 3rd day morning and 5th day (today morning) around 10 am when she got up and both came negative. She is feeling fatigue and very much stressed about all this. There were yellowish discharge from her vagina right before her last periods.  So please give me your opinion on what might be happening and what I should do next. Hoping for a reply at the earliest.