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MEME-FIMO return different count of target for the same sequence

Hi, I have a motif of 48bp which is presented by a letter-probability matrix. I scanned this motif using the FIMO program of MEME suite in a DNA sequence which length is about 600Mb and some other smaller subsequences truncated from the prior huge sequence. But I got different target numbers in the subsequences and the same regions in the huge sequence. I used default parameters for running the FIMO program. I would much appreciate if you could kindly help me.

meme fimo motif-scan
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written by 1406104889 • 1406104889

I think your background model will be different for whole genome and its fragments. And that might be the reason for the differences in motif detection.

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written by Satyajeet Khare Satyajeet Khare

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