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
22435	3'	-56.3	NC_005056.1	+	12071	0.66	0.48117
	Target:  5'- aUCGCagagCUGGuuauuC-CGCCGGAGGUGGg- -3' miRNA:   3'- -AGUGg---GACCu----GuGUGGCCUUCACCag -5'
22435	3'	-56.3	NC_005056.1	+	10418	0.67	0.450141
	Target:  5'- aUCGaCCUGaACcagcuacccGCACCGGAuGUGGUCg -3' miRNA:   3'- -AGUgGGACcUG---------UGUGGCCUuCACCAG- -5'
22435	3'	-56.3	NC_005056.1	+	21611	0.68	0.382314
	Target:  5'- -gACCgUGGAgcuUACACCGGcguaacggcaAAGUGGUUa -3' miRNA:   3'- agUGGgACCU---GUGUGGCC----------UUCACCAG- -5'
22435	3'	-56.3	NC_005056.1	+	17615	0.72	0.222606
	Target:  5'- aUUACCCUGGACAauCCGGucaagcGUGGUg -3' miRNA:   3'- -AGUGGGACCUGUguGGCCuu----CACCAg -5'
22435	3'	-56.3	NC_005056.1	+	17813	0.73	0.188768
	Target:  5'- -gACCUUGuGGCGCugGCCGGuaAGGUGGUCg -3' miRNA:   3'- agUGGGAC-CUGUG--UGGCC--UUCACCAG- -5'
22435	3'	-56.3	NC_005056.1	+	21232	0.84	0.02769
	Target:  5'- aCACCg-GGGCGCGCCGGAuGUGGUCa -3' miRNA:   3'- aGUGGgaCCUGUGUGGCCUuCACCAG- -5'
22435	3'	-56.3	NC_005056.1	+	9873	1.1	0.000349
	Target:  5'- gUCACCCUGGACACACCGGAAGUGGUCu -3' miRNA:   3'- -AGUGGGACCUGUGUGGCCUUCACCAG- -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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