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
9362	3'	-53.5	NC_002512.2	+	165490	0.67	0.976613
	Target:  5'- uCGGGuggCUGcGCGuGGggcgCUUCU-CCCg -3' miRNA:   3'- -GCCCuuaGAC-CGCuCCa---GAAGAaGGG- -5'
9362	3'	-53.5	NC_002512.2	+	97520	0.69	0.946997
	Target:  5'- uCGGG-AUCgUGGCGuGcGUCUaCUUCUCg -3' miRNA:   3'- -GCCCuUAG-ACCGCuC-CAGAaGAAGGG- -5'
9362	3'	-53.5	NC_002512.2	+	132705	0.69	0.942633
	Target:  5'- aCGGGcGUCgugGGCGAGaUCcUCggCCCg -3' miRNA:   3'- -GCCCuUAGa--CCGCUCcAGaAGaaGGG- -5'
9362	3'	-53.5	NC_002512.2	+	223115	0.71	0.90568
	Target:  5'- gGGGGAUCcgcgGGuCGAGuccGUCaucgUCUUCCCg -3' miRNA:   3'- gCCCUUAGa---CC-GCUC---CAGa---AGAAGGG- -5'
9362	3'	-53.5	NC_002512.2	+	89430	0.71	0.886436
	Target:  5'- uCGGGcGUC-GGCGGGGUCacgUCcgggCCCa -3' miRNA:   3'- -GCCCuUAGaCCGCUCCAGa--AGaa--GGG- -5'
9362	3'	-53.5	NC_002512.2	+	90556	0.71	0.878887
	Target:  5'- gCGGGAGgacgagGGCGAgggcgacggccccGGUCUcCUUCCCc -3' miRNA:   3'- -GCCCUUaga---CCGCU-------------CCAGAaGAAGGG- -5'
9362	3'	-53.5	NC_002512.2	+	155378	0.78	0.537383
	Target:  5'- gCGGGAccgcgaggCUGGCGAGGUCcUCUccgUCCUg -3' miRNA:   3'- -GCCCUua------GACCGCUCCAGaAGA---AGGG- -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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