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
21971	3'	-57.5	NC_004914.1	+	45673	0.66	0.622124
	Target:  5'- uUCCGUCGCuucagucaUGCGGUUGauGGCGuAGCg -3' miRNA:   3'- uGGGCGGUGcg------ACGCCAAU--UCGC-UCG- -5'
21971	3'	-57.5	NC_004914.1	+	59411	0.66	0.589853
	Target:  5'- uACCgGUUugGCUGuCGGUgccuuucuGUGGGCu -3' miRNA:   3'- -UGGgCGGugCGAC-GCCAauu-----CGCUCG- -5'
21971	3'	-57.5	NC_004914.1	+	6220	0.67	0.547335
	Target:  5'- cCCCGUCACGCUGUGu---GGUGuacGGCu -3' miRNA:   3'- uGGGCGGUGCGACGCcaauUCGC---UCG- -5'
21971	3'	-57.5	NC_004914.1	+	1631	0.68	0.516091
	Target:  5'- aGCCCGCUcugAUGCcuaUGCGGaacaaaucaAGGCGGGCc -3' miRNA:   3'- -UGGGCGG---UGCG---ACGCCaa-------UUCGCUCG- -5'
21971	3'	-57.5	NC_004914.1	+	52442	0.7	0.390915
	Target:  5'- cGCCCgGCCcuuuaGCUcaGUGGUgaGAGCGAGCg -3' miRNA:   3'- -UGGG-CGGug---CGA--CGCCAa-UUCGCUCG- -5'
21971	3'	-57.5	NC_004914.1	+	37874	0.71	0.35656
	Target:  5'- gGCCUGCauUAUGUcGUGGUUGAGCGGGa -3' miRNA:   3'- -UGGGCG--GUGCGaCGCCAAUUCGCUCg -5'
21971	3'	-57.5	NC_004914.1	+	26494	1.1	0.000584
	Target:  5'- cACCCGCCACGCUGCGGUUAAGCGAGCc -3' miRNA:   3'- -UGGGCGGUGCGACGCCAAUUCGCUCG- -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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