How to measure the signalling speed of Gigabit optical ethernet?
You need to get a timing signal from the same system that is generating the test patterns. 

Even if two signal sources are nominally generating a 1250 MHz clock signal and a 1.25 Gbaud data signal, there is likely to be a small difference (on the order 10's of parts per million, or on the order of 1-5 kHz in your 1.25 Gbaud system) in frequency between them, and this will make one useless as a trigger for an oscilloscope measurement of the other.

Depending on what kind of scope you are using, you may be able to trigger from the data pattern rather than a separate clock signal.