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
27569	5'	-56.4	NC_005882.1	+	29804	0.66	0.505503
	Target:  5'- gCGCGGCGCUUGAccGGaCGAaccucaagcagacUGGcGGcUCg -3' miRNA:   3'- aGCGCUGCGAACU--CC-GCU-------------ACC-CCaAG- -5'
27569	5'	-56.4	NC_005882.1	+	1612	0.67	0.444482
	Target:  5'- -gGCGACGCccGAuGCGAUGGGcGUc- -3' miRNA:   3'- agCGCUGCGaaCUcCGCUACCC-CAag -5'
27569	5'	-56.4	NC_005882.1	+	14766	0.68	0.423773
	Target:  5'- cCGCGaugGCGCUgcugaugUGGGGCGGUcaGGUUCa -3' miRNA:   3'- aGCGC---UGCGA-------ACUCCGCUAccCCAAG- -5'
27569	5'	-56.4	NC_005882.1	+	952	0.68	0.405543
	Target:  5'- uUCGCGGCaucugGCUUGAgcuGGCGGaucGGGGcgUCg -3' miRNA:   3'- -AGCGCUG-----CGAACU---CCGCUa--CCCCa-AG- -5'
27569	5'	-56.4	NC_005882.1	+	26780	0.69	0.368822
	Target:  5'- gUCGCGACGCUcGcGGCcGGcUGGGGc-- -3' miRNA:   3'- -AGCGCUGCGAaCuCCG-CU-ACCCCaag -5'
27569	5'	-56.4	NC_005882.1	+	10105	0.74	0.169689
	Target:  5'- -gGCGGCGCUUGGuGCGGUGGacuugaucgcuacgcGGUUCa -3' miRNA:   3'- agCGCUGCGAACUcCGCUACC---------------CCAAG- -5'
27569	5'	-56.4	NC_005882.1	+	7861	1.1	0.000346
	Target:  5'- gUCGCGACGCUUGAGGCGAUGGGGUUCg -3' miRNA:   3'- -AGCGCUGCGAACUCCGCUACCCCAAG- -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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