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
28038	5'	-51.8	NC_005887.1	+	40819	0.66	0.817255
	Target:  5'- cUUCGCGGUCGUCGacaGCagG-UCCGGg -3' miRNA:   3'- cAAGUGCCAGUAGCa--CGagCaAGGUU- -5'
28038	5'	-51.8	NC_005887.1	+	36717	0.66	0.796221
	Target:  5'- -gUCACGucGUCGUCGUGCgaaacgauguuaaUCGUgCCGAu -3' miRNA:   3'- caAGUGC--CAGUAGCACG-------------AGCAaGGUU- -5'
28038	5'	-51.8	NC_005887.1	+	26900	0.66	0.776464
	Target:  5'- --gCGCGGUCAUCGcgGCgaCGUcgUCCGGu -3' miRNA:   3'- caaGUGCCAGUAGCa-CGa-GCA--AGGUU- -5'
28038	5'	-51.8	NC_005887.1	+	24719	0.67	0.755021
	Target:  5'- cUUCACGGcgcugacCGUCGUGCgcagCGUuUCCAu -3' miRNA:   3'- cAAGUGCCa------GUAGCACGa---GCA-AGGUu -5'
28038	5'	-51.8	NC_005887.1	+	33893	0.67	0.744084
	Target:  5'- -gUCGCcguauuGGUCGUCGUGCUCGggagugaagCCu- -3' miRNA:   3'- caAGUG------CCAGUAGCACGAGCaa-------GGuu -5'
28038	5'	-51.8	NC_005887.1	+	41210	0.68	0.664746
	Target:  5'- --cCGCGcGUCGUCGUGCcCGUgaCCGAg -3' miRNA:   3'- caaGUGC-CAGUAGCACGaGCAa-GGUU- -5'
28038	5'	-51.8	NC_005887.1	+	20393	1.07	0.002051
	Target:  5'- cGUUCACGGUCAUCGUGCUCGUUCCAAa -3' miRNA:   3'- -CAAGUGCCAGUAGCACGAGCAAGGUU- -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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