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
21830	3'	-56.3	NC_004831.2	+	38277	0.66	0.564966
	Target:  5'- gUugCAGUACCAGCauCACcguauuugauAGUUGCCAu -3' miRNA:   3'- -GugGUCGUGGUCG--GUGau--------UCAGCGGU- -5'
21830	3'	-56.3	NC_004831.2	+	22853	0.67	0.468334
	Target:  5'- aGCCAGCuuCGGCUucagGCUAucaauGUCGCCc -3' miRNA:   3'- gUGGUCGugGUCGG----UGAUu----CAGCGGu -5'
21830	3'	-56.3	NC_004831.2	+	38478	0.69	0.39007
	Target:  5'- -uCCGGCACagGGCCGCUAAGgagGCUAg -3' miRNA:   3'- guGGUCGUGg-UCGGUGAUUCag-CGGU- -5'
21830	3'	-56.3	NC_004831.2	+	31149	0.73	0.211004
	Target:  5'- -cUCGGCACCAGCCACUGc--UGCCGu -3' miRNA:   3'- guGGUCGUGGUCGGUGAUucaGCGGU- -5'
21830	3'	-56.3	NC_004831.2	+	34271	1.09	0.000501
	Target:  5'- aCACCAGCACCAGCCACUAAGUCGCCAa -3' miRNA:   3'- -GUGGUCGUGGUCGGUGAUUCAGCGGU- -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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