Motif discovery using MEME

Question

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So, I was using meme for motif discovery online (web based) and offline both version. I have used for the same set of sequences and I found that the e-values for the same motif sequences varies using meme offline and online version ,technically this shouldn’t be the case, any idea why the values are different??

[GouthamAtla]

The background frequencies used online and offline are same ?

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As far as I know it performs denovo motif discovery without any reference , and the e-value states the statistical significance of motif in the given sequence data. I am not sure about the background frequencies you are asking for, can you elaborate? Thanks

Answer 1

[Girolamo]

Is the difference in terms of e-values huge? As far as I remember, the background is calculated by shuffling the sequences in the input, hence you can have a slight difference Are the versions(online and offline) the same?