The cut-off usually depends upon the category you belong from. That being said, if considering that you belong to the General Category, and you are not a resident of Pondicherry, then the cut-off percentile is around 50. 

The cut-off is based on the percentile received in the exam. Here are the recent cutoff trends. 

Generally, for UR Non-Pondicherry candidates, the available seats are almost about 65, the breakdown of which can be reported as 50 in Pondicherry itself, and 15 in Karaikal. The top 65 rankers are rather marked safe in the list.

Now, if you look closely at the AIIMS and JIPMER merit lists, there are numerous toppers that appear in each of the respective lists. Quite clearly, at least about 30 to 35 candidates choose to leave JIPMER to enlist at AIIMS, New Delhi. 

That being said, it is quite natural that the top 100 students will secure a seat in JIPMER under the UR category. The number however can drop down if a candidate is moving to some other college.