jtag debugger dosen't finds the connected cyclon ll processor

By 'edited the post' you mean re-written it so that the discussion thread no longer makes sense. Please don't do that - just add more to the bottom...

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But when I apply power supply to the board, it boots up normally

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Boots from where? EPCS?

Yes - the JTAG chain integrity is clearly questionable. Do you have particularly long JTAG traces? Have you provided power to the USB-Blaster from the target? Are you confident in your USB-Blaster? Have you proved your USB-Blaster and cable on another board?

Cheers,

Alex