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
13055	5'	-56.4	NC_003390.1	+	8113	0.66	0.565292
	Target:  5'- cUGAuGGCCGGUCUg-GUAuGCCUgucguucuccggaaUGGCg -3' miRNA:   3'- uACU-UCGGCCAGAgaCGU-CGGA--------------ACCG- -5'
13055	5'	-56.4	NC_003390.1	+	17454	0.66	0.535628
	Target:  5'- gGUGGAGUCGaugaGUUUCUGgagguaAGCUUUGGCc -3' miRNA:   3'- -UACUUCGGC----CAGAGACg-----UCGGAACCG- -5'
13055	5'	-56.4	NC_003390.1	+	11388	0.67	0.492758
	Target:  5'- uUGAAGCCGGagg-UGguGCCgaagaUGGCg -3' miRNA:   3'- uACUUCGGCCagagACguCGGa----ACCG- -5'
13055	5'	-56.4	NC_003390.1	+	42896	0.68	0.461667
	Target:  5'- -cGAAGCaguCGG-CUCauUGUAGCCUuugUGGCa -3' miRNA:   3'- uaCUUCG---GCCaGAG--ACGUCGGA---ACCG- -5'
13055	5'	-56.4	NC_003390.1	+	26993	0.69	0.384245
	Target:  5'- gAUGAGGCCGccaUC-CUGCAGuCCgUUGGUg -3' miRNA:   3'- -UACUUCGGCc--AGaGACGUC-GG-AACCG- -5'
13055	5'	-56.4	NC_003390.1	+	39143	0.71	0.268872
	Target:  5'- -cGggGuCCGGUguauugcaucaugcCUCgGcCAGCCUUGGCg -3' miRNA:   3'- uaCuuC-GGCCA--------------GAGaC-GUCGGAACCG- -5'
13055	5'	-56.4	NC_003390.1	+	6821	1.1	0.000403
	Target:  5'- cAUGAAGCCGGUCUCUGCAGCCUUGGCa -3' miRNA:   3'- -UACUUCGGCCAGAGACGUCGGAACCG- -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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