I created a data signal and calculated the spectrum via the fft-command in MATLAB. The data-signal itself is not periodic but it is created in a way that it can be treated as one period of a periodic signal. The last sample smoothly transitions to the first one. I observe that the absolute of the spectrum strongly depends on the zero-padding before calculating the fft. If I do zero-pad the signal such that its length is a power of two, the spectrum differs severely from the one where I kept the signal unchanged. In the following pictures you can see the results.
It can be clearly seent that there is a kind of gap at the center of the channels without zero-padding. I can't explain this. I would expect the shape of both transforms to be the same. Why is that not the case here, does anyone have an idea?