Hi Raymond,
The main difference between these PRBS sequences is the repetition interval (number of bits until the same sequence repeats) and the runlength (maximum number of consecutive identical digits, also called CID). CID defines the memory requirements of your PLL. For most short-distance applications, you have 8b/10b encoding or 64b/66b (e.g. 10GbE) which defines the maximum runlength. Using a sequence with a lare CID to test a short-distance protocol is to stringent.
The patterns to be applied, as well as the jitter to be added to the input signal, are described in this document:
ftp://ftp.t11.org/t11/pub/fc/mjsq/04-101v4.pdfIt is true that several papers show BER measurements with a pure input signal (no jitter applied), but achieving BER < 1E-12 in these conditions is not sufficient to make your design work in a real life situation.
You should also check your application spec (I'm sure the USB spec gives some references for BER measurement), most short-distance standards refer to the above mentioned Fibre Channel document. SONET and other long-haul systems have much tougher specs.
Best,
Paul