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First check: Is there a peak in whatever you are plotting. The x-axis of fft output is bins. To convert into frequency, you need to know the sampling frequency. Second, since its a 5MHz signal, have you downsampled it? All of these affect the final output. 5MHz signal requires at least 10Msps...
It depends on the resolution u want for your signals. If you just want to know what all frequencies are there, then even a 128 point FFT will do.. Go for longer N only if you wish to resolve frequencies at the output.
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