Well let's first start with what uncertainty actually means. It is the measure which denotes that a specific data will not reach its destination in the required time by the mentioned amount called uncertainty. Uncertainty in a design is a result of the variations that occur in process, voltage and temperature. It models jitter, skew and any other margins that get added to the path under concern. The main source of jitter is the PLL that generates the high frequency clock signal. It is basically a short term variation of the signal with respect to its ideal position in time.
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