I think the color marks the clock domain, but I'm not sure.
The color of the Clock component waveform symbol will change based on the clock's domain, as follows:
- Digital – The waveform color is the same as a digital wire, with a black outline.
- Analog – The waveform color is the same as an analog wire, with a black outline.
- Indeterminate – The waveform color is white, with no outline.
The information is available in component datasheet : http://www.cypress.com/file/127796/download. If you have such doubts about a component, refer the datasheet of it.You can always right click on the component and open datasheet of the component.