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
11591	5'	-58.2	NC_003085.1	+	3964	0.66	0.505568
	Target:  5'- cCGGGGAUGgAGCcagacGGCCGCgCUUGc- -3' miRNA:   3'- uGUCCCUGCaUCG-----UCGGCGgGAACac -5'
11591	5'	-58.2	NC_003085.1	+	15386	0.67	0.463742
	Target:  5'- uGCAGGaGCGUgaggacgagcgucAGCAGCCgauGCCCUuucacugaggcUGUGg -3' miRNA:   3'- -UGUCCcUGCA-------------UCGUCGG---CGGGA-----------ACAC- -5'
11591	5'	-58.2	NC_003085.1	+	18366	0.67	0.435279
	Target:  5'- cGCcGGGGCGU-GCA-CCGCCCg-GUGg -3' miRNA:   3'- -UGuCCCUGCAuCGUcGGCGGGaaCAC- -5'
11591	5'	-58.2	NC_003085.1	+	23879	0.68	0.397734
	Target:  5'- --cGGGGCGUgagcgaacggcAGCAGCCGUCCa---- -3' miRNA:   3'- uguCCCUGCA-----------UCGUCGGCGGGaacac -5'
11591	5'	-58.2	NC_003085.1	+	23042	0.68	0.370976
	Target:  5'- aGCAGuGGGCGaAGCuGCCGCCggagGUGc -3' miRNA:   3'- -UGUC-CCUGCaUCGuCGGCGGgaa-CAC- -5'
11591	5'	-58.2	NC_003085.1	+	45857	0.72	0.213573
	Target:  5'- gGCAGGGACGgcGCGGCgaGUCCUg--- -3' miRNA:   3'- -UGUCCCUGCauCGUCGg-CGGGAacac -5'
11591	5'	-58.2	NC_003085.1	+	34269	1.07	0.000541
	Target:  5'- cACAGGGACGUAGCAGCCGCCCUUGUGu -3' miRNA:   3'- -UGUCCCUGCAUCGUCGGCGGGAACAC- -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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