Runes can be found in the Tower of Trials. You can find runes as high as Tier XXIII in the Tower.
Runes will also differ in rarity, with Green as the most common and Orange as the rarest.
The higher the tier the stronger the rune can also be. This is a list of runes that can be found in the game.
Please note that these are Tier XII runes, higher tier runes would be stronger.