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Depends what kind of proteins you have. If they are all known transcription factors or other known DNA binders, then maybe. There are many online tools which will predict how likely your proteins are to bind DNA, or to bind particular sequences, but I doubt there is any tool that could tell you where any random protein would bind in the genome.
Also, what genome are you interested in?
I agree. We need to know how the sequences in the multi-fasta are related. Is it the entire complement of proteins, or is it a particular subset?