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After Effects: Alpha Channels and Traveling Mattes
In After Effects:
Choose File->Project Settings...
     Select Frames, this is easier to view than timecode.

Choose Composition->New Composition
           Input a resolution such as: width height 1920x1080, 1280x720 16:9, 640x480 4:3
           Select Square Pixels
           Set the Frame Rate to 30 fps frames per second animation or less depending on source video
           Set Start Frame to (not 0)
           Set Duration to 150 (5 seconds) etc

Choose Layer->New Text  Type a word, adjust the size, makethe text whit.

Choose File->Import->File  to bring in an image sequence or movie for the background
     If the file is an animation sequence, check TIFF sequence
     If the file has no 000 padding check Force Alphabetical order
     If the file has an alpha channel, an Interpret Footage window will pop up
          Select Premultiplied - Matted With Color: Typically black if background is black.
         
You can always change this setting later using File->Interpret Footage Main

Select the text with the Arrow Selection tool at the top.  AE_selection_arrow

Select Window->Motion Sketch, you will use this to interactively animate your type.
          Click the Start Capture button
          Drag your type around the Comp1 window.

Hit the arrow playback button to see your results.

Set your Time Marker on the Timeline to the first frame.

Make sure you are in the Project tab  (Window->Project if you don't see it)
Drag your movie on to the Timeline.
     Drag it below the type, see diagram below.

Go to the Mode/Track Matte section on the Timeline. If you do not see it hold down the right mouse over Parent and add Columns->Mode. You can hide Parent.

Click and hold on the button that reads None across from the movie; switch it to Alpha Matte.
Notice the text layer is turned off.

aftereffects1.jpg

Part 2  Complex Layers

Make another composition:Composition->New Composition

Drag Comp1 from the Project Widow into Comp2 on the Timeline.

Run an Effect such as Distort->Polar Coordinates on Comp1 in the Timeline for Comp2.
Notice the type appears to be swimming through the effect. The results would be much different if you ran the effect on the type alone in Comp1.