The clean output of the Producer is intended to be used for post-production, where certain elements of the main production output are not needed (e.g. graphics). While the main Producer output contains every element sent out to the Program (live), only those elements routed to the clean output will be visible in both the dirty and the clean feeds.
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Having the option to send specific assets such as live sources without commentary to a separate DVR recorder maximizes the value you get from your live productions without the need for additional Producers or streams.