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The foundation of a hole punch cloud is traditionally a mid- or high-altitude cloud type such as cirrus or cirro-stratus. Such clouds generally form above 20,000 feet or so in the atmosphere. The National Weather Service has explained that such clouds are frequently composed of both ice crystals and super-cooled water droplets – water that is below the freezing temperature but still exists in liquid form. When such a delicate balance occurs, only a slight disruption of this delicate balance may lead to a striking result.
It is believed that a cloud may be disrupted in this manner when a a jet flies through the thin cloud layer. Such a disruption may spur the quick freezing of liquid droplets and evaporation of other droplets. This would create the void in the space in which the jet passed through the layer.