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I am using combining JTAG and Active Serial Configurations schemes. I have added 120 Ohms resistor between lines DATA, DCLK, nCS, ASDI of flash memory and FPGA like starter kit Altera cyclone II.
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You should rather refer to the circuits suggested in the Cyclone II Hardware Handbook. The "Can't not recognize the silicon ID" error is unspecific, it simply tells that the programmer can't connect to the serial flash. Without seeing the complete schematic related to AS configuration, I won't guess about possible reasons.
Besides programming the serial flash through the dedicated AS interface, you can also use indirect JTAG programming. It requires conversion of the configuration to a *.jic file.
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