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Life is not all about JEE MAIN or ADVANCED. Its a long time in your hand to prepare well. And Do score good in boards also. don't neglect it.
Many students don't bother boards.Remember these marks will always help you in upcoming studies or internships or any job interview. As per your goal you know very well what to do. So don't get demoralized if you get low marks. If IITs and NITs your main concern do try next year and don't forget to appear in others competitive exams also.
BEST OF LUCK:)