In my h/w secondary SCL & SDA lines are connected to RTC chip. I'm not able to see the clock & data on the i2c bus using logic analizer. Will i2c work with secondary lines.
I'm not sure what you want to do. Please take a look at sections 50.2.2 Block Diagram, 50.2.4 Signal Descriptions and the PINCFG bit-field description in the RM rev.9.
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