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
9880	5'	-56.8	NC_002641.1	+	52083	0.66	0.880467
	Target:  5'- aUGGGCcaACAUUC-UUCCCuUCGCCUu -3' miRNA:   3'- -ACCCGcgUGUAAGuGAGGGcAGUGGA- -5'
9880	5'	-56.8	NC_002641.1	+	68002	0.67	0.842666
	Target:  5'- aUGGGcCGCcgauGCGUUCAaagaUCCUuauGUCGCCUu -3' miRNA:   3'- -ACCC-GCG----UGUAAGUg---AGGG---CAGUGGA- -5'
9880	5'	-56.8	NC_002641.1	+	128847	0.68	0.791153
	Target:  5'- aUGGGCuCGCAUgaGCUCCCGugauuUCACUa -3' miRNA:   3'- -ACCCGcGUGUAagUGAGGGC-----AGUGGa -5'
9880	5'	-56.8	NC_002641.1	+	153626	0.68	0.791153
	Target:  5'- aUGGGCuCGCAUgaGCUCCCGugauuUCACUa -3' miRNA:   3'- -ACCCGcGUGUAagUGAGGGC-----AGUGGa -5'
9880	5'	-56.8	NC_002641.1	+	140931	0.72	0.583265
	Target:  5'- aUGGGUGUguGCAUgauaACUCUCGUCACUUu -3' miRNA:   3'- -ACCCGCG--UGUAag--UGAGGGCAGUGGA- -5'
9880	5'	-56.8	NC_002641.1	+	112812	0.76	0.362488
	Target:  5'- cGGGCGCACGUUacaauagcaGCgugCCCGUUAUCUa -3' miRNA:   3'- aCCCGCGUGUAAg--------UGa--GGGCAGUGGA- -5'
9880	5'	-56.8	NC_002641.1	+	109407	1.07	0.003155
	Target:  5'- aUGGGCGCACAUUCACUCCCGUCACCUc -3' miRNA:   3'- -ACCCGCGUGUAAGUGAGGGCAGUGGA- -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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