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
28437	3'	-55.8	NC_005946.1	+	97233	0.66	0.86994
	Target:  5'- --aGGGGGCugggGCUCuGGGGu-CUUGGg -3' miRNA:   3'- gaaCCCUCGca--UGAG-CCCCuuGGACC- -5'
28437	3'	-55.8	NC_005946.1	+	15602	0.66	0.865401
	Target:  5'- -cUGaGGAGCGUucacccugcucucgaGCUCGuuGAGCUUGGa -3' miRNA:   3'- gaAC-CCUCGCA---------------UGAGCccCUUGGACC- -5'
28437	3'	-55.8	NC_005946.1	+	24936	0.66	0.854509
	Target:  5'- --cGGGAGCGaucaUGCUCaGGGcuccGGCgUGGa -3' miRNA:   3'- gaaCCCUCGC----AUGAGcCCC----UUGgACC- -5'
28437	3'	-55.8	NC_005946.1	+	47004	0.67	0.826402
	Target:  5'- gUUGGGAGCGUACUCuaaccacuCUUGGa -3' miRNA:   3'- gAACCCUCGCAUGAGccccuu--GGACC- -5'
28437	3'	-55.8	NC_005946.1	+	102199	0.71	0.603228
	Target:  5'- --cGGGGGCGUcuGCguaGGGGAACCcGa -3' miRNA:   3'- gaaCCCUCGCA--UGag-CCCCUUGGaCc -5'
28437	3'	-55.8	NC_005946.1	+	57949	0.73	0.501816
	Target:  5'- --cGGGAggGUGUACgUGGGGAacgugGCCUGGa -3' miRNA:   3'- gaaCCCU--CGCAUGaGCCCCU-----UGGACC- -5'
28437	3'	-55.8	NC_005946.1	+	86959	0.97	0.015658
	Target:  5'- uCUUGGGAGCGUACUC-GGGAACCUGGc -3' miRNA:   3'- -GAACCCUCGCAUGAGcCCCUUGGACC- -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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