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Scales are not over the skin, they are part of the skin. Snake sheds are only clear on lighter colored snakes; dark snakes such as my Argentine boa constrictors have darker sheds. However, the true reason why sheds are so much lighter than the animal, is that they are merely one layer of skin with the tiny amount of pigment found on one layer. All the layers on top of one another create the darker look of the snake. Sheds are also darker on snakes with more heavily keeled or otherwise rough scales.
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