Hello aspirant,

Autonomous colleges are the private colleges which are not run by the state or it doesn't fall under the government; rather falls under its own jurisdictions . The fees are considerably way higher than the government medical colleges.
The exams too are conducted by the university. This means all the colleges affiliated to the same university will have same question papers and will be evaluated by same people with same criteria. Autonomous colleges on the other hand are granted freedom and in some or all the matters.

I hope that this will help.