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
10642	3'	-56.8	NC_002702.1	+	10501	0.67	0.428661
	Target:  5'- -------gCGACGGCGGCGCUGAgGAa -3' miRNA:   3'- cuacagagGCUGUCGUCGCGGCUgCU- -5'
10642	3'	-56.8	NC_002702.1	+	10610	0.69	0.304932
	Target:  5'- --gGUUUCUGGCGGuCAGCGCC-AUGAu -3' miRNA:   3'- cuaCAGAGGCUGUC-GUCGCGGcUGCU- -5'
10642	3'	-56.8	NC_002702.1	+	14017	0.7	0.277891
	Target:  5'- cGUGaCUCaGACAGCAcccgcggcccccgccGCGCCGGCGGu -3' miRNA:   3'- cUACaGAGgCUGUCGU---------------CGCGGCUGCU- -5'
10642	3'	-56.8	NC_002702.1	+	16140	0.76	0.103686
	Target:  5'- ---cUCUCC-ACAGUAGCGCCGACGc -3' miRNA:   3'- cuacAGAGGcUGUCGUCGCGGCUGCu -5'
10642	3'	-56.8	NC_002702.1	+	21115	1.08	0.000416
	Target:  5'- gGAUGUCUCCGACAGCAGCGCCGACGAc -3' miRNA:   3'- -CUACAGAGGCUGUCGUCGCGGCUGCU- -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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