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If you use the IP generated as a PRBS pattern mode datapath with external loopback connection using the megawizard (i.e Cy IV fig 1-74 transceiver arch spec) , do you need to take care of the synchronization/alignment manually or these megawizard generated blocks do everything for you except for connectivity to the pins.
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That is yet another PRBS pattern generator/checker. Altera have IP cores that you can use in the fabric too.
I haven't used these features of the transceivers, since they are basically hard-wired, i.e., if you select that feature in the transceiver IP block, you cannot actually use it for transmission or reception.
Create an instance of the ALTGX component with that option selected, and I'm sure there must be some status signals that indicate whether or not pattern errors are generated.
Personally I prefer implementing that checking logic in the fabric, as then I can transmit actual data as well.
The Altera PRBS generator/checker is described in (Ch 35 or 36)
http://www.altera.com/literature/ug/ug_embedded_ip.pdf Cheers,
Dave