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
21894	3'	-62.8	NC_004902.1	+	9115	0.67	0.260257
	Target:  5'- cGCCgAGCAUCaUGCCaugCUUCCaaaaaGCCUGc -3' miRNA:   3'- -UGGgUCGUAG-ACGGa--GGAGGg----CGGGC- -5'
21894	3'	-62.8	NC_004902.1	+	40461	0.67	0.247539
	Target:  5'- cCCCAGgug--GaCCUCCuUCCCGCCCa -3' miRNA:   3'- uGGGUCguagaC-GGAGG-AGGGCGGGc -5'
21894	3'	-62.8	NC_004902.1	+	12406	0.68	0.212453
	Target:  5'- --gCGGCGUCUGCCUCUUCCUuggugaucuguGCCa- -3' miRNA:   3'- uggGUCGUAGACGGAGGAGGG-----------CGGgc -5'
21894	3'	-62.8	NC_004902.1	+	26925	0.68	0.207039
	Target:  5'- aGCCCAuGCAggcCUGCCUCCUcaugaaaaCCUGUagCCGg -3' miRNA:   3'- -UGGGU-CGUa--GACGGAGGA--------GGGCG--GGC- -5'
21894	3'	-62.8	NC_004902.1	+	32589	0.69	0.186562
	Target:  5'- uCCCAGCuugCaaggGCCUgagucaCCUCCuCGCCCGu -3' miRNA:   3'- uGGGUCGua-Ga---CGGA------GGAGG-GCGGGC- -5'
21894	3'	-62.8	NC_004902.1	+	11910	0.72	0.11199
	Target:  5'- aGCUCAGUG-CUGCCUguUCUUCUGCCCGg -3' miRNA:   3'- -UGGGUCGUaGACGGA--GGAGGGCGGGC- -5'
21894	3'	-62.8	NC_004902.1	+	34572	1.08	0.00016
	Target:  5'- aACCCAGCAUCUGCCUCCUCCCGCCCGa -3' miRNA:   3'- -UGGGUCGUAGACGGAGGAGGGCGGGC- -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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