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When I try to make a gif with two frames both of which have a transparent background in GIMP, what happens is that the first frame looks OK, then the second frame appears on top of it, such that you can see both frames at the same time.

How can I make animated gif in which all of the frames have a transparent background but each time a frame appears, the previous frame disappears completely ?

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When exporting/saving (depends on version) your work as GIF, you have several options for it. One way for that, what you probably want, could be done by choosing from "Frame disposal where unspecified" option "One frame per layer (replace)".

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For the current version (2.8.0), in the name for each frame layer, include (replace). For example:

frame 1(250ms)(replace)

That will tell gimp to replace instead of stacking. Note that you can use the stacking for some pretty cool effects as well.

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