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
31626	5'	-56.4	NC_006879.1	+	9827	0.66	0.498806
	Target:  5'- -aGCGGGaGAGCcaggUGAUGC-CGGCCgagGUg -3' miRNA:   3'- gcUGUCC-CUCG----ACUACGuGUCGGa--CG- -5'
31626	5'	-56.4	NC_006879.1	+	9901	0.67	0.446553
	Target:  5'- -cGCAGGGGGCgaaagcgcuccaUGGUGgGCAcGCuCUGCc -3' miRNA:   3'- gcUGUCCCUCG------------ACUACgUGU-CG-GACG- -5'
31626	5'	-56.4	NC_006879.1	+	26025	0.67	0.446553
	Target:  5'- aCGGCAGuGAuGCaGAUGuCGCAGCCgaGCu -3' miRNA:   3'- -GCUGUCcCU-CGaCUAC-GUGUCGGa-CG- -5'
31626	5'	-56.4	NC_006879.1	+	20162	0.69	0.32658
	Target:  5'- gCGugAGcGGAGUUGgcGUACAGCauguuCUGCc -3' miRNA:   3'- -GCugUC-CCUCGACuaCGUGUCG-----GACG- -5'
31626	5'	-56.4	NC_006879.1	+	15145	0.69	0.318404
	Target:  5'- uGACGGGaguccGAGUgccGGUGCGCAGCCg-- -3' miRNA:   3'- gCUGUCC-----CUCGa--CUACGUGUCGGacg -5'
31626	5'	-56.4	NC_006879.1	+	22254	0.78	0.07363
	Target:  5'- uGGgAGGGAGCUGAgGCGCcuCCUGCu -3' miRNA:   3'- gCUgUCCCUCGACUaCGUGucGGACG- -5'
31626	5'	-56.4	NC_006879.1	+	11113	1.12	0.000205
	Target:  5'- gCGACAGGGAGCUGAUGCACAGCCUGCa -3' miRNA:   3'- -GCUGUCCCUCGACUACGUGUCGGACG- -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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