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I have a signal in MATLAB on which I'd like to perform an FFT. My signal is stored in s, and I use the code below (inspired by the MATLAB help):

L = length(s);
nfft = 2^nextpow2(L);
S = fft(s,nfft)/L;
fftf = 1/Ts/2*linspace(0,1,nfft/2+1);
ffts = (2*abs(S(1:nfft/2+1)));

My signal s is a GMSK-modulated one, that is, it varies between $f_c-2.4e3$ and $f_c+2.4e3$ in my case when transmitting 0 or 1, respectively. $f_c$ is set to 100kHz. For a long input, say, 250 bits worth of 1's and 250 bits worth of 0's, I get what I expect, see the first image below.

If I instead choose a low number of bits, say 10 1 bits followed by 10 0 bits, I get as expected, but it is shifted down to ~90kHz instead of centered at 100kHz. This is something I can't quite understand - it seems changing the sample rate and length of the FFT changes absolutely nothing.

Can anyone explain to me why? Thanks in advance!

EDIT: I'm not allowed to post pictures, so here's some links instead.

Long data: http://f.cl.ly/items/0R1i0x0m46221A230m25/fft1.png

Short data: http://f.cl.ly/items/2a320I2l2r3M1i2o2N11/fft1.png

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closed as off topic by Asaf Karagila, Davide Giraudo, Alexander Gruber, Dilip Sarwate, Stefan Hansen Feb 21 '13 at 12:23

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I feel that this question may benefit more on a programming related site. –  Asaf Karagila Feb 21 '13 at 11:38
@Asaf It's one thing to feel this way, and quite another to say the question is off-topic. Is signal processing not mathematics? –  user53153 Feb 21 '13 at 12:35
@5pm: Depends who you're asking. Sometimes set theory is not mathematics... :-) If I could vote to migrate to SO I would. –  Asaf Karagila Feb 21 '13 at 12:38
I chose math.stackexchange.com because I figured my mistake was mathematical rather than a programming error. But I guess I can try somewhere else.. –  Tausen Feb 21 '13 at 12:40
Without trying it out (don't have matlab) I can guess this is related to the signal being padded to the length that is a power of 2. Padding from 500 to 512 in the first example is a small matter, but in the second it's from 20 to 32. This discussion may be helpful. –  user53153 Feb 21 '13 at 13:07

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