Basys 3 400MHz Logic
The circuits on the board have internal PLLs. These are blocks that can generate a signal (like a clock) that is related to the reference (in this case the reference is the 100 MHz oscillator), but not necessarily equal. There are various ways to implement these blocks, but almost all big digital circuits will contain one (or more) to create clocks based off a reference. 

One of the benefits is that a PLL can usually change the ratio between the generated signal and the reference. This means you can use a single, fixed reference, yet still change your clock speed of the digital circuit (for example to achieve lower power)