I missed my period for 4 months before my boyfriend and I started having sex. 12 days ago we had unprotected sex and 5 days after I noticed spots of blood on my tissue every time I wiped my urine since them I have been experiencing terrible lower back pains. Could I be pregnant or its some kind of infection?

Yes it could be either or neither, it is far to early to tell about pregnancy. In about 30 days, if you have not had a period, try a home pregnancy test.