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
30899	3'	-57.5	NC_006552.1	+	33289	0.66	0.61487
	Target:  5'- gGCAGUAGGCGgAauuGAUCGCgugggcgaUGGuGGc -3' miRNA:   3'- -UGUCGUCCGCgU---CUAGCGag------ACCuCC- -5'
30899	3'	-57.5	NC_006552.1	+	58797	0.67	0.582644
	Target:  5'- cCAGCAGGCGCcgcacaUGCcUUGGGGGu -3' miRNA:   3'- uGUCGUCCGCGucua--GCGaGACCUCC- -5'
30899	3'	-57.5	NC_006552.1	+	46695	0.67	0.571971
	Target:  5'- uGCAGCGGGgGauGGUCGCuugccugaUCUGGAGc -3' miRNA:   3'- -UGUCGUCCgCguCUAGCG--------AGACCUCc -5'
30899	3'	-57.5	NC_006552.1	+	53258	0.67	0.561344
	Target:  5'- uCAGCgAGGC-C-GAg-GCUCUGGAGGg -3' miRNA:   3'- uGUCG-UCCGcGuCUagCGAGACCUCC- -5'
30899	3'	-57.5	NC_006552.1	+	4253	0.68	0.519455
	Target:  5'- -aGGCAGGCGCAuaguuuccCGCUUUGGcGGu -3' miRNA:   3'- ugUCGUCCGCGUcua-----GCGAGACCuCC- -5'
30899	3'	-57.5	NC_006552.1	+	209	0.68	0.488863
	Target:  5'- aGCAGCccaucgaacccaAGGCGCuuGAUCGC-CUGGuugauGGu -3' miRNA:   3'- -UGUCG------------UCCGCGu-CUAGCGaGACCu----CC- -5'
30899	3'	-57.5	NC_006552.1	+	32096	0.72	0.311556
	Target:  5'- gGCAcCAGGCGCAGcgaaguGUCGCcCUGGAuGGc -3' miRNA:   3'- -UGUcGUCCGCGUC------UAGCGaGACCU-CC- -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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