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
30872	5'	-55.1	NC_006552.1	+	35162	0.66	0.775791
	Target:  5'- --cGCGAacaaGCCGGcgGCCUGUUGGAu -3' miRNA:   3'- ugaCGCUagg-UGGUCa-UGGACAGCCU- -5'
30872	5'	-55.1	NC_006552.1	+	13595	0.66	0.74225
	Target:  5'- gGCUGCGGUCC-CC-GUcuuccuugcgcugcGCCUuGUCGGc -3' miRNA:   3'- -UGACGCUAGGuGGuCA--------------UGGA-CAGCCu -5'
30872	5'	-55.1	NC_006552.1	+	22304	0.67	0.703246
	Target:  5'- gUUGCcuGAUCCACCAGcaggugcGCCgGUCGGu -3' miRNA:   3'- uGACG--CUAGGUGGUCa------UGGaCAGCCu -5'
30872	5'	-55.1	NC_006552.1	+	46636	0.68	0.616432
	Target:  5'- gACgGCGAUCCACUGGaUGCCgaugaaGUCGaGAu -3' miRNA:   3'- -UGaCGCUAGGUGGUC-AUGGa-----CAGC-CU- -5'
30872	5'	-55.1	NC_006552.1	+	9954	0.7	0.530379
	Target:  5'- cGCguggGCGAUCCGCagggGGUcuGCCUGUCGa- -3' miRNA:   3'- -UGa---CGCUAGGUGg---UCA--UGGACAGCcu -5'
30872	5'	-55.1	NC_006552.1	+	12187	0.71	0.468797
	Target:  5'- --gGUGG-CgGCCAGUGCCUuGUCGGAc -3' miRNA:   3'- ugaCGCUaGgUGGUCAUGGA-CAGCCU- -5'
30872	5'	-55.1	NC_006552.1	+	33645	0.71	0.449085
	Target:  5'- --aGCGGUCaCGCCGGcACCgaagugGUCGGAa -3' miRNA:   3'- ugaCGCUAG-GUGGUCaUGGa-----CAGCCU- -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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