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
21747	5'	-55.8	NC_004813.1	+	25866	0.66	0.647739
	Target:  5'- -gCggUUGGCUGUGguGCgcugUGGCUGGc -3' miRNA:   3'- caGuuGACCGACACguCGa---GUCGGUC- -5'
21747	5'	-55.8	NC_004813.1	+	37852	0.66	0.647739
	Target:  5'- cGUCA---GGCUGcUGCGGC--AGCCAGg -3' miRNA:   3'- -CAGUugaCCGAC-ACGUCGagUCGGUC- -5'
21747	5'	-55.8	NC_004813.1	+	37325	0.67	0.603031
	Target:  5'- cGUCAggcACUGgaacugaucGCUGaUGCAGagUCGGCCAGa -3' miRNA:   3'- -CAGU---UGAC---------CGAC-ACGUCg-AGUCGGUC- -5'
21747	5'	-55.8	NC_004813.1	+	46146	0.67	0.569734
	Target:  5'- --aAGCUGGCUGUugucuauCAGCUCccacagccccugAGCCAGa -3' miRNA:   3'- cagUUGACCGACAc------GUCGAG------------UCGGUC- -5'
21747	5'	-55.8	NC_004813.1	+	22113	0.7	0.377041
	Target:  5'- uUCGAaaUGGC-GUGaCAGCUCAGCCAc -3' miRNA:   3'- cAGUUg-ACCGaCAC-GUCGAGUCGGUc -5'
21747	5'	-55.8	NC_004813.1	+	47912	0.71	0.33404
	Target:  5'- uUCAGCUGGaUUGUGCAGUUCuguaCCGGu -3' miRNA:   3'- cAGUUGACC-GACACGUCGAGuc--GGUC- -5'
21747	5'	-55.8	NC_004813.1	+	37972	1	0.003037
	Target:  5'- -gUAACUGGCUGUGCAGCUCAGCCAGa -3' miRNA:   3'- caGUUGACCGACACGUCGAGUCGGUC- -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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