What you see is fft leakage ..
I don't know how you generate the sine output , I suspect if you use a simple funktion generator vi the output frequency migth be coerced ...
FIRST: make shure you use a common timebase 😉
If you need to generate ,capture and measure any frequency/phase/amplitude without SR 'limitation' to n periodes in m sample (for higher n and m the deviation can be quite small) you need to use continious generation while feeding new values to the output and use sine fitting on your input.
If you go the n periodes in m sample way, you can use the FFT with m or multiple m sample window length (and rec window)
EDIT: If you use the same SR for generation and capture, you migth run into the problem that you generate a new value at the same time you want to sample. minor glitches can give noisy or not phase stable results. but you can configure different delays or slopes in the timing clock properties.. (don't expext that with a sigmadelta converter but who knows ..)
Greetings from Germany
Henrik
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