Jacki
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Hello,
I think it depends how you design your clock divider. Normally it is based on DFF, so the output should be square wave. If you use other analog solution to get your frequency divider, probably you get the sinewave at the output, but it is large signal, I don't know which kind of circuit can give you the sinewave with such big output swing. About the phase difference, it is normal to have the phase offset (you can consider it as DC offset). With the phase offset (constant phase difference), your PLL is still locked and works. If you use charge pump based PLL, you may get spurs at the output spectrum. If you want to remove the phase offset, you need high enough loop gain, and matching current sources in your charge pump.
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