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Repeat your urine pregnancy
test with first morning sample after 1 week to confirm pregnancy.If you have late conception pregnancy test will come positive late.There are many causes of painful intercourse in your case it could be due to infection [PID].If your vaginal discharge
is curdy white or yellowish,bad smell,if you have itching then it is not normal consult a doctor for examination and treatment.
I hope this answer is helpful to you.