As a gas planet, it's not exactly surprising that Jupiter is famous for its storms and clouds—indeed, Jupiter's most famous feature, the Great Red Spot, is a storm that's lasted perhaps 400 years and is at least twice the size of Earth. By those standards, the rare breaks in Jupiter's swirling cover are tiny, but they provide our best chance to see the planet's deeper secrets.
Admittedly, "tiny" is a relative measure, as these cloudless areas are on average the size of North America. Known as hot spots, these regions have long intrigued astronomers for the view they provide into otherwise hidden layers of Jupiter's atmosphere. Some of these hot spots might allow us to peer down to where water clouds form. In the video up top, NASA scientist David Choi explains how the Cassini spacecraft has allowed astronomers to track the movement and formation of the hot spots like never before, revealing that they actually share some similarities with weather patterns here on Earth. Data from Cassini has allowed NASA scientists to put together time-lapse movies of the hot spots in action.
As for why these cloud-free areas are known as hot spots, here's an explanation straight from NASA:
In pictures, hot spots appear shadowy, but because the deeper layers are warmer, hot spots are very bright at the infrared wavelengths where heat is sensed; in fact, this is how they got their name.
One hypothesis is that hot spots occur when big drafts of air sink in the atmosphere and get heated or dried out in the process. But the surprising regularity of hot spots has led some researchers to suspect there is an atmospheric wave involved. Typically, eight to 10 hot spots line up, roughly evenly spaced, with dense white plumes of cloud in between. This pattern could be explained by a wave that pushes cold air down, breaking up any clouds, and then carries warm air up, causing the heavy cloud cover seen in the plumes.
For more, check out the Jet Propulsion Laboratory website.