I was 5 days late on my periods and when I got my periods I had them for only 1 day. Now I am having pain in my lower left side of stomach. Now I see little brown spots on the toilet paper when I wipe. I got home pregnancy test done and its negative. I want to know if I can still be pregnant.

Are you on birth control at all? Sometimes that can cause irregular periods. Implantation bleeding is common in early pregnacny and you can have small amounts of brown blood/discharge when you wipe. It is not good to have pain on just one side of your stomach however. If you feel you may be pregnant, wait a week and re-test. However if the pain you have is bad and continues I would see your doctor.