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You can free up your upload storage space by deleting submissions with file uploads on them.
However, upon checking your account, I see that you have a form with a lot of submissions that is moved in the "Trash" folder, this means that that form and its submissions are still in your account. You need to delete that form by clicking "Purge".
Please note that purging the form will delete the form itself and its submissions permanently, which means they will not be restored or recovered.
What I would suggest is that you recover or restore that form first by following this guide: http://www.jotform.com/help/134-How-to-Restore-Deleted-Forms.
Then navigate to your submissions page and download your submissions and the uploads so that you have a backup of them for future reference
After that, you can safely delete your submissions from there to free up your upload space.
I would also like to suggest that you integrate the available file sharing and storage service apps (ex. Google Drive, Dropbox, Box.net) found in this page: http://apps.jotform.com/category/file_sharing_and_storage
I hope that helps.