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
22000	5'	-51.1	NC_004914.1	+	2133	0.67	0.900407
	Target:  5'- -gGGUUCAGGUgaaaGUCgGGCGGguAAGCCGu -3' miRNA:   3'- gaCCGAGUUUAg---CAG-UCGCU--UUCGGC- -5'
22000	5'	-51.1	NC_004914.1	+	55861	0.67	0.900407
	Target:  5'- -gGGCagAAGUgGUCAGCGAugcggaGGGaCCGg -3' miRNA:   3'- gaCCGagUUUAgCAGUCGCU------UUC-GGC- -5'
22000	5'	-51.1	NC_004914.1	+	54801	0.67	0.898283
	Target:  5'- uCUGGCgCAAcagaaggcgcugagGUCGUCGGaCGGuuGCCu -3' miRNA:   3'- -GACCGaGUU--------------UAGCAGUC-GCUuuCGGc -5'
22000	5'	-51.1	NC_004914.1	+	11576	0.67	0.885773
	Target:  5'- uCUGGCggcggCAGguaaucccauGUCGcCAGgGAAGGCCc -3' miRNA:   3'- -GACCGa----GUU----------UAGCaGUCgCUUUCGGc -5'
22000	5'	-51.1	NC_004914.1	+	57308	0.69	0.816943
	Target:  5'- -gGGCUCAccagcgcuGAaCGUCAGCGucugaaAGAGCUGg -3' miRNA:   3'- gaCCGAGU--------UUaGCAGUCGC------UUUCGGC- -5'
22000	5'	-51.1	NC_004914.1	+	52495	0.7	0.724391
	Target:  5'- gCUGGUUCAAAUC--CAGCaAGGGCCa -3' miRNA:   3'- -GACCGAGUUUAGcaGUCGcUUUCGGc -5'
22000	5'	-51.1	NC_004914.1	+	46171	1.09	0.003078
	Target:  5'- uCUGGCUCAAAUCGUCAGCGAAAGCCGu -3' miRNA:   3'- -GACCGAGUUUAGCAGUCGCUUUCGGC- -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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