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Hi, thanks for your response. But I am only concerned about this is because acceptance letter from the University wasn't missing but that has been stated as the reason for rejection. My University has also confirmed that the format of the letter that they sent me is their standard format that they have been using previously. Do you have any other thoughts regarding this?

All you can do is call or send a CSE. I would attach the acceptance letter to the CSE and tell them that this letter was attached originally. That is your best bet.