Alright.
Pure chakra is the result of moulding the physical and spiritual energies. Once moulded, pure chakra is produced. This chakra doesn't have any special characteristics or abilities unless given them when the user changes the properties of the chakra to give it an element. To increase the amount of chakra available, a ninja must constantly train to build experience, and as a result more chakra will become ready to use. There are two ways to manipulate chakra when using ninjutsu: Shape Transformation (this involves control of the movement, form and strength of the chakra being manipulated) and Nature Transformation (this involves changing the properties of the chakra and giving it an element. This also includes Yin-Yang manipulation which means the balancing of the ratio between Yin and Yang chakra within a jutsu e.g. during Naruto's Bijuu training, when he was learning how to create a Bijuudama.
Elemental chakra is created by manipulating ones chakra into an element that they have an affinity for. There are five different types of elemental chakra: Fire, Wind, Lightning, Earth and Water. As previously explained, each element has a weakness against one, but a strength against another. For example, if a Katon and Suiton technique of the same level would clash, the Suiton jutsu would win because it is the superior element. However, if a Katon and a Suiton technique of different level were to clash, and in this instance the Katon technique was of greater strength, the Katon technique would win.
While there are elements that are strong against one and weak against another, there are elements that are neutral against each other. In other words, if two techniques of the same element and power were to clash, they would both be negated. Though if these techniques were the same element but one was stronger than the other, the stronger one would triumph. Also, the technique that won the clash would not only defeat the other jutsu, it would also gain power from the defeated technique, and the user of the defeated technique would take more damage, since the winning technique gained in power.
Every ninja has an affinity for a certain element, this means that they will have better skill using that element than a ninja who doesn't have an affinity for the element. An example of this is the Uchiha Clan, they were a clan famous for their affinity and mastery of Katon/Fire Release. To see what elemental affinity a ninja has, they will use a piece of paper that reacts to small amounts of chakra activity. The reaction that the paper takes will vary.
-If Fire, the paper will burn to ash.
-If Water, the paper will dampen and become wet.
-If Earth, the paper will crumble away as dirt.
-If Lightning, the paper will wrinkle.
-If Wind, the paper will split in two.
Ninja aren't just limited to one affinity, they can have two elemental affinities as well. Ninja can also master all 5 elements without having an affinity for all of them, though they will face great difficulty doing so. Rinnegan users have the ability to manipulate all 5 elements. Kakuzu was able to use the Basic 5 through stealing people's hearts, and Hiruzen was able to use all 5 through only training.
Besides the Basic 5 elements, there are also many other elements that can be made via mixing two elements. Though this ability is rare to find without the use of a Kekkei Genkai or Kekkei Tota, there are ninja who have developed other elements without a Kekkei Genkai or Tota.
The other elements include:
-Ice Release: this requires Water and Wind and is a Kekkei Genkai.
-Wood Release: this requires Earth and Water and is a Kekkei Genkai.
-Lava Release: this requires Earth and Fire and is a Kekkei Genkai as well as a Bijuu skill.
-Blaze Release: it is unknown what elements are required, but it is an advanced manipulation of Amaterasu. It is an MS skill.
-Storm Release: this requires Water and Wind and is a Kekkei Genkai.
-Dust Release: this requires Fire, Earth and Wind and is a Kekkei Tota.
-Scorch Release: this requires Fire and Wind and is a Kekkei Genkai.
-Magnet Release: it is unknown what elements are required, it is a Kekkei Genkai.
-Steel Release: this requires Earth and Fire and is a Kekkei Genkai.
-Swift Release: this requires Wind and Lightning and is a Kekkei Genkai.
-Blast Release: this requires Earth and Lightning and is a Kekkei Genkai.
-Dark Release: this doesn't require any elements, it is a Kekkei Genkai.
-Yin-Yang Release: this isn't an element, though it has two branching elements, Yin Release and Yang Release.
Hand seals are used to perform Ninjutsu, Genjutsu and other techniques that exclude Taijutsu. Performing these seals helps to manipulate the amount of chakra needed in a technique and each jutsu has a different sequence of these seals. While some ninja may need to perform every hand seal for the technique, the number is either drastically lessened or isn't needed when a skilled ninja performs the technique. An example of this is Sasuke's Chidori, in Part I he needed to perform every hand seal and by the end of Part I that number lessened to a total of 3 seals. By Part II, he could make a Chidori without the use of seals and could utilize Katon techniques with only one handseal. While it is rare, some ninja can perform hand seals with only one hand, e.g. Haku, Minato and Guren.
So thats why it took almost two hours 0_0, sorry if its really long, I tried to divide it into paragraphs instead of just a wall of text. Hope this is alright.