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You can try miRanda as it requires only the RNA sequences and a genome fasta file.
http://cbio.mskcc.org/microrna_data/manual.html
i think it is not working or i could not find the way , actually i just want to find prediction. i would be appreciate if you could help me about it...
There is a version at conda you can use I guess. https://anaconda.org/bioconda/miranda
Thank you so much, i will definitely try it.