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
29183	5'	-53.9	NC_006150.1	+	77761	0.66	0.975678
	Target:  5'- --cGCCAagCGcUCCgUGGCGAGACGUu -3' miRNA:   3'- caaCGGUcaGU-AGGgACCGUUCUGUA- -5'
29183	5'	-53.9	NC_006150.1	+	146834	0.66	0.973031
	Target:  5'- --cGUCAGUCAcagucuUCCCcGGuCGAGACGc -3' miRNA:   3'- caaCGGUCAGU------AGGGaCC-GUUCUGUa -5'
29183	5'	-53.9	NC_006150.1	+	202670	0.67	0.93939
	Target:  5'- -cUGUCAGUCAUCCg-GGCAgcccugAGGCGc -3' miRNA:   3'- caACGGUCAGUAGGgaCCGU------UCUGUa -5'
29183	5'	-53.9	NC_006150.1	+	190176	0.68	0.934478
	Target:  5'- --cGCCAGUUuaaacugCCCUGGCAA-ACAUu -3' miRNA:   3'- caaCGGUCAGua-----GGGACCGUUcUGUA- -5'
29183	5'	-53.9	NC_006150.1	+	218026	0.68	0.92932
	Target:  5'- --gGCCGGaUCAUCUgaGGCcAGACAg -3' miRNA:   3'- caaCGGUC-AGUAGGgaCCGuUCUGUa -5'
29183	5'	-53.9	NC_006150.1	+	207717	0.69	0.899861
	Target:  5'- --aGCCAGgc--CCCUGGCAcGGCGUg -3' miRNA:   3'- caaCGGUCaguaGGGACCGUuCUGUA- -5'
29183	5'	-53.9	NC_006150.1	+	168936	0.7	0.864477
	Target:  5'- -cUGUCGGUCAUCugggccgcuguCCUGGCAAGuCGg -3' miRNA:   3'- caACGGUCAGUAG-----------GGACCGUUCuGUa -5'
29183	5'	-53.9	NC_006150.1	+	92837	1.07	0.007284
	Target:  5'- cGUUGCCAGUCAUCCCUGGCAAGACAUg -3' miRNA:   3'- -CAACGGUCAGUAGGGACCGUUCUGUA- -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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