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Transparency notes
On the Sega Genesis and NES the first color for each row is transparent.
When you import a png file it may contain transparent data. It is better to use a png file with transparency than a mask color however a mask color will also work if that color is the first color for affected palette rows.
When the same color occurs multiple times in the same palette row the last color will be used. You can take advantage of this if you want the transparent color to be the same as a solid color. In sonic one the sprite of sonic uses black for transparency and solids. This also applies to all sprites that share the same palette with sonic. The reason this works is due to the fact that transparent pixels are always assigned to color 0. Therefore any non transparent pixels will not use said transparent color.