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    $\begingroup$ There are too many things left unsaid and unspecified in this answer. Mohammad is essentially assuming a circular shift of the data without saying so. See @JasonR's (edited) answer for a careful description of this point, and my comment on the main question saying that there are many ways of using the FFT and they all give different results $\endgroup$ Commented Oct 26, 2011 at 17:27
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    $\begingroup$ @DilipSarwate is right, this is assuming a circular shift of data. As he pointed out there are subtleties in the FFT based on the input vector. $\endgroup$ Commented Oct 26, 2011 at 17:50
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    $\begingroup$ @gallamine, may I ask what your data vectors looks like, exmaple: - Signal1: [someZeros, signal, someZeros] - Signal2: [someDifferentNumberOfZeros, signal, someDifferentNumberOfZeros] $\endgroup$ Commented Oct 26, 2011 at 17:53