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
6302	3'	-52.9	NC_001844.1	+	116058	0.66	0.965326
	Target:  5'- gCGggGCCGaCCAGaaCCUGgccCAguucugCCAGAa -3' miRNA:   3'- -GCuuUGGC-GGUC--GGACaa-GUa-----GGUCU- -5'
6302	3'	-52.9	NC_001844.1	+	90657	0.67	0.954305
	Target:  5'- gCGAAaaGCCGCCuGUgUGUUaggcgguaccUAUCCAGGu -3' miRNA:   3'- -GCUU--UGGCGGuCGgACAA----------GUAGGUCU- -5'
6302	3'	-52.9	NC_001844.1	+	116346	0.67	0.94113
	Target:  5'- uCGGAACCuGCCAGCgcgagccgCUGcUCAcaccaUCCGGAg -3' miRNA:   3'- -GCUUUGG-CGGUCG--------GACaAGU-----AGGUCU- -5'
6302	3'	-52.9	NC_001844.1	+	52863	0.69	0.895018
	Target:  5'- uGAcuUUGCgAGCCUGUaucccagcaUCAUCCAGGc -3' miRNA:   3'- gCUuuGGCGgUCGGACA---------AGUAGGUCU- -5'
6302	3'	-52.9	NC_001844.1	+	113692	0.72	0.76005
	Target:  5'- gGAGuACCGCCAGCggGUUCugCCAGAc -3' miRNA:   3'- gCUU-UGGCGGUCGgaCAAGuaGGUCU- -5'
6302	3'	-52.9	NC_001844.1	+	18556	0.73	0.699581
	Target:  5'- gCGggGCCGCUuuugagguggcGCCgaacaaGUUCAUCCGGAg -3' miRNA:   3'- -GCuuUGGCGGu----------CGGa-----CAAGUAGGUCU- -5'
6302	3'	-52.9	NC_001844.1	+	122653	0.76	0.522931
	Target:  5'- -----aCGCCAGCCU-UUCAUCCAGAg -3' miRNA:   3'- gcuuugGCGGUCGGAcAAGUAGGUCU- -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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