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
22076	3'	-57.1	NC_004927.1	+	34297	0.67	0.687964
	Target:  5'- cGCuuGaCCGugUUCCCC-UUCCCGAa- -3' miRNA:   3'- -CGu-CaGGCugAAGGGGuAGGGGCUcu -5'
22076	3'	-57.1	NC_004927.1	+	32279	0.67	0.656503
	Target:  5'- uGUAGUCaacguCGGCUUCCCaCGaCUUCGAGAa -3' miRNA:   3'- -CGUCAG-----GCUGAAGGG-GUaGGGGCUCU- -5'
22076	3'	-57.1	NC_004927.1	+	6435	0.67	0.656503
	Target:  5'- aCAGUCa-GCUUCCCCcacuucUCCCCGGu- -3' miRNA:   3'- cGUCAGgcUGAAGGGGu-----AGGGGCUcu -5'
22076	3'	-57.1	NC_004927.1	+	11124	0.67	0.63541
	Target:  5'- -gAGUCCGugUcCCUCGUCCacaaucaCGAGGu -3' miRNA:   3'- cgUCAGGCugAaGGGGUAGGg------GCUCU- -5'
22076	3'	-57.1	NC_004927.1	+	51802	0.69	0.57233
	Target:  5'- gGCGGUCggugagcgugCGAC-UCCCCAUCugaCUCGGGAa -3' miRNA:   3'- -CGUCAG----------GCUGaAGGGGUAG---GGGCUCU- -5'
22076	3'	-57.1	NC_004927.1	+	6122	0.71	0.424388
	Target:  5'- uGCcGUCCGGgUUUCCCAuccagUCCUCGGGGu -3' miRNA:   3'- -CGuCAGGCUgAAGGGGU-----AGGGGCUCU- -5'
22076	3'	-57.1	NC_004927.1	+	46356	1.11	0.000843
	Target:  5'- cGCAGUCCGACUUCCCCAUCCCCGAGAu -3' miRNA:   3'- -CGUCAGGCUGAAGGGGUAGGGGCUCU- -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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