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
28484	5'	-61.9	NC_005946.1	+	41676	0.66	0.494089
	Target:  5'- cAGGGCcuCCCUGGUCUuuacaaucuGCCUGaGCa-- -3' miRNA:   3'- cUCCCGu-GGGACCAGA---------UGGAC-CGggu -5'
28484	5'	-61.9	NC_005946.1	+	30812	0.67	0.465801
	Target:  5'- cGGGGGCAUCUUaacggccaGGUCUgucuuuACCagGGCCCu -3' miRNA:   3'- -CUCCCGUGGGA--------CCAGA------UGGa-CCGGGu -5'
28484	5'	-61.9	NC_005946.1	+	41948	0.67	0.447416
	Target:  5'- gGGGGGUAUCuCUGacccGUCUGCgaUGGCCCu -3' miRNA:   3'- -CUCCCGUGG-GAC----CAGAUGg-ACCGGGu -5'
28484	5'	-61.9	NC_005946.1	+	8024	0.68	0.394806
	Target:  5'- cGGGaGgACCCUGGcUCcguCCUGGCCUg -3' miRNA:   3'- cUCC-CgUGGGACC-AGau-GGACCGGGu -5'
28484	5'	-61.9	NC_005946.1	+	95421	0.69	0.338717
	Target:  5'- uAGGGuCugCUgGGUCUGCUUGGCUCc -3' miRNA:   3'- cUCCC-GugGGaCCAGAUGGACCGGGu -5'
28484	5'	-61.9	NC_005946.1	+	61282	0.69	0.338717
	Target:  5'- aAGGGgAUCCUGuGcuUCUguagguACCUGGCCCAg -3' miRNA:   3'- cUCCCgUGGGAC-C--AGA------UGGACCGGGU- -5'
28484	5'	-61.9	NC_005946.1	+	71805	0.71	0.269034
	Target:  5'- cAGGGCcguaGCCCUGaagCUcCCUGGCCCu -3' miRNA:   3'- cUCCCG----UGGGACca-GAuGGACCGGGu -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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