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but it would be nice to add a JTAG header to that system as well so i can quickly test new designs, and only use the boot off the micro controller once im happy and the board works standalone
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Yes, so you have already answered the question yourself.
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can the two be combined? i had a quick read of the AN 250 doc but could not find any examples of boot from micro controller combined with JTAG or AS header
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JTAG configuration and debugging functions are available in any configuration mode. AS mode is alternative to PS. You need switches or jumpers for MSEL to select between both.