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
31477	3'	-46.4	NC_006653.1	+	11142	0.66	0.913943
	Target:  5'- ---aUCGUGUGCUUcgAUGGCAUUUu -3' miRNA:   3'- aaaaAGUAUACGGGaaUACCGUAGGc -5'
31477	3'	-46.4	NC_006653.1	+	17733	0.67	0.898706
	Target:  5'- aUUUUUAUucuacGCCUUUAUGGCAUaCGa -3' miRNA:   3'- aAAAAGUAua---CGGGAAUACCGUAgGC- -5'
31477	3'	-46.4	NC_006653.1	+	4075	0.73	0.582833
	Target:  5'- uUUUUUUAUAcGCCUUUAUGGC-UCCc -3' miRNA:   3'- -AAAAAGUAUaCGGGAAUACCGuAGGc -5'
31477	3'	-46.4	NC_006653.1	+	18206	0.73	0.582833
	Target:  5'- uUUUUUUAUAcGCCUUUAUGGC-UCCc -3' miRNA:   3'- -AAAAAGUAUaCGGGAAUACCGuAGGc -5'
31477	3'	-46.4	NC_006653.1	+	5697	0.78	0.336552
	Target:  5'- aUUUUUAuucUAUGCCUUUAUGGCAUuuGu -3' miRNA:   3'- aAAAAGU---AUACGGGAAUACCGUAggC- -5'
31477	3'	-46.4	NC_006653.1	+	3605	0.83	0.15944
	Target:  5'- aUUUUUAUGauacGCCUUUAUGGCAUCCGa -3' miRNA:   3'- aAAAAGUAUa---CGGGAAUACCGUAGGC- -5'
31477	3'	-46.4	NC_006653.1	+	18294	1.02	0.00839
	Target:  5'- uUUUUUCAUAUGCUCUUAUGGCAUCCGa -3' miRNA:   3'- -AAAAAGUAUACGGGAAUACCGUAGGC- -5'
31477	3'	-46.4	NC_006653.1	+	4163	1.08	0.002999
	Target:  5'- uUUUUUCAUAUGCCCUUAUGGCAUCCGa -3' miRNA:   3'- -AAAAAGUAUACGGGAAUACCGUAGGC- -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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