miRNA display CGI

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ID	Location	Perfect MFE.*	RefSeq Acc.	strand	Start Position	R_P_ratio#	P value
	Predicted miRNA align pattern
8662	5'	-45.7	NC_002229.2	+	135707	1.07	0.033994
	Target:  5'- aACAGUGGCACACAUCAAACAAAGUAAa -3' miRNA:   3'- -UGUCACCGUGUGUAGUUUGUUUCAUU- -5'
8662	5'	-45.7	NC_002229.2	+	121029	0.66	0.999949
	Target:  5'- --cGUGGCAUAUcuGUCGAuCGAAGUGc -3' miRNA:   3'- uguCACCGUGUG--UAGUUuGUUUCAUu -5'
8662	5'	-45.7	NC_002229.2	+	65482	0.68	0.99942
	Target:  5'- -aGGUGGCACACcauauaucuuuaugGUCAGACAuGGa-- -3' miRNA:   3'- ugUCACCGUGUG--------------UAGUUUGUuUCauu -5'
8662	5'	-45.7	NC_002229.2	+	37704	0.71	0.99611
	Target:  5'- -aAGUGGCAUGCAUCAAAUAu----- -3' miRNA:   3'- ugUCACCGUGUGUAGUUUGUuucauu -5'
8662	5'	-45.7	NC_002229.2	+	3004	1.07	0.033994
	Target:  5'- aACAGUGGCACACAUCAAACAAAGUAAa -3' miRNA:   3'- -UGUCACCGUGUGUAGUUUGUUUCAUU- -5'

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Note:
      When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.

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