Dear Pierre-Yves,
Actually you should use a clock above 3MHz as there are transformers and you are likely to be filtered out, or in non linearity zone at 100kHz. You would need a DC coupled card to go under 3MHz
The data is indeed left aligned, on your previous post you were masking out the 4 MSB bits which is obviously not correct, you should shift the samples to the right and not remove 4 bits out of the 12 bits, looking at the graph on your old post, it looks to me as if you have missing bits.
I think you should go back to the initial software, don't tamper with samples and the number of bits. Actually the samples are left aligned because then you have a sign bit which is convenient, of course the samples have a bigger value but otherwise one would need to implement sign extension. Also leave matlab a side so far, it is too easy to wrongly represent the samples. I would initially recommend you to use a fantastic tool made by Analog Devices. This tool is called Visual Analog and is free of charge. I am attaching a Visual Analog project file which is actually able to use buffer generated by our FMC10xAPP. But this assume you have the initial software where the samples are left aligned without any bits masked out.
Place a 10MHz signal, 2Vpp centered on 0V, run FMC10xApp, launch Visual Analog, open the project, browse to your buffer and press the run button. You will see the time domain but also frequency domain and FFT post analysis.
Best Regards,
Arnaud
http://www.analog.com/en/converters-tools/adc-tools/topic.html <== Visual Analog can be downloaded from there.