exporting format for texture

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I'm going to ask a really stupid question (to avoid myself hours of heartbreak)...

can you have transparancy in a texture? I.e. could you have a colour (for example bright purple RGB=255,0,255) set to transparant (by using 'maskimage' or somesuch) on a texture, and get transparancy on that colour?

What I'm thinking about doing is createing a skybox with stripes of transparancy, making two layers and rotating it to get a crazy 'moray fringe' or optical illusion type-effect.

I.e. for the bottom layer I don't want uniform transparancy for the layer, rather bits of it that are completely transparant, and other bits that are completely opaque. So I don't THINK that merely setting the alpha for the object will do.