What is JotForm?
JotForm is a free online form builder which helps you create online forms without writing a single line of code. No sign-up required.
At JotForm, we want to make sure that you’re getting the online form builder help that you need. Our friendly customer support team is available 24/7.
We believe that if one user has a question, there could be more users who may have the same question. This is why many of our support forum threads are public and available to be searched and viewed. If you’d like help immediately, feel free to search for a similar question, or submit your question or concern.
I am not sure if I have understood your question correctly.
Do you want to add a unique confirmation number in your submission / auto-responder email?
You can take advantage of our "Unique ID" widget. You can add this widget in your form which will generate a unique id for every submission. You also have option to customize the unique id by adding prefix and number padding. Once you have this field in your form, you can add it in your submission email as well. The following guide should help you: http://www.jotform.com/help/79-Add-Custom-Unique-IDs-to-your-Form-Submissions
Hope this helps.
Do get back to us if you meant to ask something else.