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
31552	5'	-56.6	NC_006820.1	+	154432	0.66	0.920116
	Target:  5'- gACgCCUCcugUGACgccugcagCgCCUCCauaCAAUCCCa -3' miRNA:   3'- -UG-GGAGa--ACUGa-------G-GGAGGg--GUUAGGG- -5'
31552	5'	-56.6	NC_006820.1	+	164455	0.66	0.908085
	Target:  5'- cGCCCUCguuauagggGAgUCCucuaacaCUCCCCAuAUCCUc -3' miRNA:   3'- -UGGGAGaa-------CUgAGG-------GAGGGGU-UAGGG- -5'
31552	5'	-56.6	NC_006820.1	+	155947	0.67	0.889848
	Target:  5'- aAUCCUCU--ACcuaaUCUCCCCAAUCCUu -3' miRNA:   3'- -UGGGAGAacUGag--GGAGGGGUUAGGG- -5'
31552	5'	-56.6	NC_006820.1	+	24766	0.67	0.876204
	Target:  5'- cACCUUCgggUGAC-CCCUaCCCCA-UCgCa -3' miRNA:   3'- -UGGGAGa--ACUGaGGGA-GGGGUuAGgG- -5'
31552	5'	-56.6	NC_006820.1	+	84488	0.69	0.778524
	Target:  5'- uUCUUCUUGACUUCUUCUaCUGAUCCUa -3' miRNA:   3'- uGGGAGAACUGAGGGAGG-GGUUAGGG- -5'
31552	5'	-56.6	NC_006820.1	+	4206	0.7	0.760126
	Target:  5'- uACCCUUUUGAgaUCCUUCUUCaAGUCCUg -3' miRNA:   3'- -UGGGAGAACUg-AGGGAGGGG-UUAGGG- -5'
31552	5'	-56.6	NC_006820.1	+	22261	1.12	0.002204
	Target:  5'- cACCCUCUUGACUCCCUCCCCAAUCCCg -3' miRNA:   3'- -UGGGAGAACUGAGGGAGGGGUUAGGG- -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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