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
13610	5'	-54.1	NC_003460.1	+	4977	0.7	0.076727
	Target:  5'- aCGAAgGCCG-CUCAGGCGAcaauuGCAcGCCGu -3' miRNA:   3'- -GUUUgUGGUaGGGUCCGCU-----UGU-CGGC- -5'
13610	5'	-54.1	NC_003460.1	+	1630	1.08	5.3e-05
	Target:  5'- gCAAACACCAUCCCAGGCGAACAGCCGc -3' miRNA:   3'- -GUUUGUGGUAGGGUCCGCUUGUCGGC- -5'
13610	5'	-54.1	NC_003460.1	+	1531	0.72	0.052302
	Target:  5'- aCGAcCACCAgagcaCCCAcGGCGAaaGCGGCCa -3' miRNA:   3'- -GUUuGUGGUa----GGGU-CCGCU--UGUCGGc -5'
13610	5'	-54.1	NC_003460.1	+	3451	0.72	0.055901
	Target:  5'- -cAGgGCCGaggguucUCCCAGuCGAGCAGCCGg -3' miRNA:   3'- guUUgUGGU-------AGGGUCcGCUUGUCGGC- -5'
13610	5'	-54.1	NC_003460.1	+	2935	0.68	0.125482
	Target:  5'- gCGAGCAUCuuaaacagCCAGGCGAACAucagcgaucaccgccGCCGg -3' miRNA:   3'- -GUUUGUGGuag-----GGUCCGCUUGU---------------CGGC- -5'
13610	5'	-54.1	NC_003460.1	+	5712	0.66	0.167028
	Target:  5'- aGGACACCcgCCU-GGCGGcgGGCCu -3' miRNA:   3'- gUUUGUGGuaGGGuCCGCUugUCGGc -5'
13610	5'	-54.1	NC_003460.1	+	676	0.66	0.167028
	Target:  5'- cCAAGCACCcgaCCAaccCGAGCAGCCu -3' miRNA:   3'- -GUUUGUGGuagGGUcc-GCUUGUCGGc -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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