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Chakra is the moulding of the physical energy. It is present in every cell of the body and the spiritual energy gained from exercise and experience. Once moulded, it can be channelled through the chakra circulatory system, which is to chakra as the regular circulatory system is to blood, to any of the 361 chakra points (called tenketsu) in the body. Through various methods, the most common of which is hand seals, the chakra can then be manipulated to create an effect that would not be possible otherwise, such as walking on water, exhaling fire or creating illusions.
Ninjutsu Is a term used for any technique. allows the user to do something that they otherwise would be incapable of doing, including the usage of weapons. Ninjutsu and Genjutsu are deadly but the difference between the two is that ninjutsu is real. Ninjutsu most of the time relies on chakra and hand seals. Ninjutsu could also be used to heal others and to manipulate nature.