Yes, i understand your query as i would like to give you a brief about this as follows :

utonomous colleges are deemed or self controlling ones, they do not come under any university, for instance madras medical college is affiliated to dr.MGR university in tamil nadu, but sri ramchandra medical college is a deemed university and they dont come under any. they conduct their own exams and they have their own ste of rules, its not universal. and the fee structure would be costly too. its always good to get in to govt affiliated colleges as it is considered prestigious , even in many parts of the world and when u appear for PG exams abroad. so make a wise choice. hope this helps. good luck buddy