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Hello Anjana,
Yes you can apply for only a single one of these.
The seats of government medical and dental colleges are divided into 2 quotas-
1. All India Quota - 15%
2. State Quota - 85%
You can apply for both or either one of these quotas but for applying for the state quota, you need to be of that state, i.e, you should have done your education in that state board.
The dates of counselling for both these quotas is different in colleges so it is upto you if you want to apply for one or both of these quotas.
Hope this helps.
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