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A subsequence is a sequence that is used as a part of another sequence (its "parent sequence", or "the main sequence"). The subsequence is represented in the main sequence as a channel, with a special device type of "Sequence", as opposed to "Light-O-Rama controller", "X10 controller", or so forth.
For example, the following Channel Settings dialog shows a channel that is a subsequence:
Channel settings for a subsequence
A channel for a subsequence can be turned on and off, using the Sequence Editor, in the same ways that other channels can be. When the channel in the main sequence is turned on, the subsequence will begin playing, from its beginning. It will continue playing for as long as the channel remains on; if play of the subsequence reaches its end before the channel has been turned off in the main sequence, the subsequence will simply loop back to its beginning and continue playing.
When the channel in the main sequence is turned off, the subsequence will stop playing. If the channel is subsequently turned back on, the subsequence will start playing again, from its beginning (not from the last point that it left off at).
If you have the Animator open, it will not show the play of your subsequence. Only the events in your main sequence will be displayed. This only affects the display in the Animator; your actual lights will reflect play of both the main sequence and its subsequences.
Tip: Do not set up the same physical unit and circuit to be a channel in a sequence and a channel in a subsequence of that sequence (or two channels in two different subsequences of a sequence). Doing so will likely cause unexpected and undesired results, as the two channels compete for control over the same physical circuit.
Tip: Consider using the new Paint Sequence tool instead of subsequences; it can be used to accomplish some of the same things as subsequences, without the extra complication, and perhaps in a more obvious way. As opposed to subsequences, the effects generated via Paint Sequence really do become effects in the sequence being painted into, and are displayed in regular channels of the sequence just like any other effects in the sequence. The main advantage remaining to subsequences is that if you update the effects in the subsequence file, the change will take place in the main sequence as well. If this is not necessary or desired, Paint Sequence may be a better, easier, and clearer choice.