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1. I thought that I can use those switches for input in my schemes, not JTAG settings since this is written in schematic:
https://image.ibb.co/fyKG4y/Screen_Shot_2018_07_02_at_2_16_57_AM.png And this is the only thing I found about JTAG and AS:
https://image.ibb.co/kD89Py/Screen_Shot_2018_07_02_at_2_17_06_AM.png 2. Thank you very much for this, I understand how to do this and it will be an easier problem to solve when I put everything into place to work properly.
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Ok, so it looks like those four switches are just for user data input, have nothing to do with configuration.
Re: configuration, your device is probably setup for AS configuration from a board EPCS-compatible flash EEPROM (the MSELx pins will set this up).
However, JTAG configuration should be able to override this and you should be able to download a .sof file directly to the FPGA sram configuration. Since that is not working, I recommend using the programmer software JTAG debugger tools to validate your JTAG interface is working correctly. Under the programmer 'Tools' menu there is the 'JTAG Chain Debugger' selection you can use to validate that basic JTAG is working, or not.
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