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
18401	3'	-48.6	NC_004681.1	+	35884	0.66	0.982363
	Target:  5'- -aCUGGGAUgcacgGGCUCCAUCcucGAAUCc -3' miRNA:   3'- ugGACCUUG-----CUGAGGUAGauaCUUAG- -5'
18401	3'	-48.6	NC_004681.1	+	19836	0.66	0.981694
	Target:  5'- ---cGGGGCGAUcagcaacggccugaUCCAUgUGUGGAUCa -3' miRNA:   3'- uggaCCUUGCUG--------------AGGUAgAUACUUAG- -5'
18401	3'	-48.6	NC_004681.1	+	50699	0.67	0.97754
	Target:  5'- uCCUGGAgcACGGCUaCAUCUAcGAAc- -3' miRNA:   3'- uGGACCU--UGCUGAgGUAGAUaCUUag -5'
18401	3'	-48.6	NC_004681.1	+	70785	0.72	0.845308
	Target:  5'- aACCaUGGAGCGAUUgaCCGUCUGaGggUUa -3' miRNA:   3'- -UGG-ACCUUGCUGA--GGUAGAUaCuuAG- -5'
18401	3'	-48.6	NC_004681.1	+	66707	0.72	0.817545
	Target:  5'- aGCCggugGGAAUGACgUCCAcagUCUGUGGcuuGUCa -3' miRNA:   3'- -UGGa---CCUUGCUG-AGGU---AGAUACU---UAG- -5'
18401	3'	-48.6	NC_004681.1	+	39331	0.77	0.566745
	Target:  5'- cGCgCUGGAcACGGCUCCGaggggccgCUGUGGAUCg -3' miRNA:   3'- -UG-GACCU-UGCUGAGGUa-------GAUACUUAG- -5'
18401	3'	-48.6	NC_004681.1	+	19032	1.09	0.006352
	Target:  5'- cACCUGGAACGACUCCAUCUAUGAAUCc -3' miRNA:   3'- -UGGACCUUGCUGAGGUAGAUACUUAG- -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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