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
27487	3'	-56.5	NC_005872.1	+	18195	0.67	0.357358
	Target:  5'- aUAUCGGcACAGCCaCGuccACCcaaaCUCCAGCa -3' miRNA:   3'- aAUGGUC-UGUCGG-GU---UGGc---GAGGUCG- -5'
27487	3'	-56.5	NC_005872.1	+	21194	0.67	0.339679
	Target:  5'- -gACgGGuGCGGCCCAagggGCCGCggCGGCu -3' miRNA:   3'- aaUGgUC-UGUCGGGU----UGGCGagGUCG- -5'
27487	3'	-56.5	NC_005872.1	+	13902	0.68	0.314366
	Target:  5'- -cGCCG--UGGCCCAcauaGCCGCgCCAGCc -3' miRNA:   3'- aaUGGUcuGUCGGGU----UGGCGaGGUCG- -5'
27487	3'	-56.5	NC_005872.1	+	3263	0.68	0.298299
	Target:  5'- gUUGCCGGGCAcGCCCcggguGCCGUggggggCGGCa -3' miRNA:   3'- -AAUGGUCUGU-CGGGu----UGGCGag----GUCG- -5'
27487	3'	-56.5	NC_005872.1	+	11967	0.68	0.290507
	Target:  5'- -aGCCAGcAUAG-CCAGCCGCauauagagCCGGCc -3' miRNA:   3'- aaUGGUC-UGUCgGGUUGGCGa-------GGUCG- -5'
27487	3'	-56.5	NC_005872.1	+	12917	0.69	0.24709
	Target:  5'- -gACCAGACAGacuauuUCCAGCUacCUCCAGUa -3' miRNA:   3'- aaUGGUCUGUC------GGGUUGGc-GAGGUCG- -5'
27487	3'	-56.5	NC_005872.1	+	11262	1.08	0.000267
	Target:  5'- aUUACCAGACAGCCCAACCGCUCCAGCc -3' miRNA:   3'- -AAUGGUCUGUCGGGUUGGCGAGGUCG- -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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