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
31347	5'	-41.3	NC_006623.1	+	125492	0.66	1
	Target:  5'- -cGAGCGGg---ACAGGGccGGCGUa -3' miRNA:   3'- caUUUGUCaaaaUGUUCCauUCGCAc -5'
31347	5'	-41.3	NC_006623.1	+	125208	0.66	1
	Target:  5'- -cAAACGcGUUUU--GAGGUAAGCGg- -3' miRNA:   3'- caUUUGU-CAAAAugUUCCAUUCGCac -5'
31347	5'	-41.3	NC_006623.1	+	512	0.67	1
	Target:  5'- -gAAGCGGa---GCGAGGUaggGAGUGUGg -3' miRNA:   3'- caUUUGUCaaaaUGUUCCA---UUCGCAC- -5'
31347	5'	-41.3	NC_006623.1	+	131821	0.69	0.999999
	Target:  5'- gGUAG--GGUUUUGCGAGGccagGGGUGUGc -3' miRNA:   3'- -CAUUugUCAAAAUGUUCCa---UUCGCAC- -5'
31347	5'	-41.3	NC_006623.1	+	146116	0.72	0.999971
	Target:  5'- -cGAACGGUUggaACGGGGUGGGCu-- -3' miRNA:   3'- caUUUGUCAAaa-UGUUCCAUUCGcac -5'
31347	5'	-41.3	NC_006623.1	+	115496	0.72	0.999971
	Target:  5'- -cGAACGGUUggaACGGGGUGGGCu-- -3' miRNA:   3'- caUUUGUCAAaa-UGUUCCAUUCGcac -5'
31347	5'	-41.3	NC_006623.1	+	115360	1.1	0.073706
	Target:  5'- gGUAAACAGUUUUACAAGGUAAGCGUGc -3' miRNA:   3'- -CAUUUGUCAAAAUGUUCCAUUCGCAC- -5'
31347	5'	-41.3	NC_006623.1	+	146252	1.1	0.073706
	Target:  5'- gGUAAACAGUUUUACAAGGUAAGCGUGc -3' miRNA:   3'- -CAUUUGUCAAAAUGUUCCAUUCGCAC- -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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