Hello there!
The admission into any college is determined by a lot of factors such as the no. of candidates, level of the entrance test, etc. Computer Science is one of the streams which is in the highest demand. Considering that and the last few year statistics, it is highly unlikely for you to CSE in the Manipal main campus because the admissions into CSE branch close by ranks around below 2500. Admission into IT is, however, easier as compared to getting admission into CSE. The rank cut off for IT is generally around 3000 to 3500. However, since your rank is way higher than the usual cut off rank, it is highly unlikely for you to get either of the two branches in the main campus of Manipal University. 
All the very best for all your future endeavors. 
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