cpanel and most other control panels also have the ability to backup to a remote FTP server, so if your on a fixed IP, you could easily run your own server and have the backup automatically transfered to that server each night.
If your not on a fixed IP, then you would need a DDNS server, and to hope that the IP didn't change part way through transfering a backup. If your familier with perl, you could install that locallly, and have a perl script running on either a cron job or a scheduled task (depending on OS) to transfer the backup for you. But that would be very dependant on the access you have to your account. Perl can easily transfer files using scp. sftp or standard ftp with the correct CPAN modules installed.
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