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
8838	3'	-61.1	NC_002484.1	+	16040	0.66	0.444824
	Target:  5'- uCGGCGg---GGACGaCUCCgauGGAGAACGg -3' miRNA:   3'- -GCCGCgagaCCUGC-GGGG---CCUCUUGC- -5'
8838	3'	-61.1	NC_002484.1	+	44767	0.67	0.408487
	Target:  5'- aGGCGCaUCgaGGAaauccaacCGCCCCGGuucgcGGGGCa -3' miRNA:   3'- gCCGCG-AGa-CCU--------GCGGGGCC-----UCUUGc -5'
8838	3'	-61.1	NC_002484.1	+	35632	0.68	0.357603
	Target:  5'- uGGCGCUUucacauacaUGGAcCGCCUgauUGGuGAGCGg -3' miRNA:   3'- gCCGCGAG---------ACCU-GCGGG---GCCuCUUGC- -5'
8838	3'	-61.1	NC_002484.1	+	3688	0.68	0.318718
	Target:  5'- aGGuCGCaCUGGACGCCCgagcgCGGGcGAACc -3' miRNA:   3'- gCC-GCGaGACCUGCGGG-----GCCU-CUUGc -5'
8838	3'	-61.1	NC_002484.1	+	19304	0.7	0.263276
	Target:  5'- uGGCGCaugcacaUGcGGCGCCCCGGAGu--- -3' miRNA:   3'- gCCGCGag-----AC-CUGCGGGGCCUCuugc -5'
8838	3'	-61.1	NC_002484.1	+	33989	0.71	0.221422
	Target:  5'- aGGCGUUCUGGuCuaCCCGGAaGugGg -3' miRNA:   3'- gCCGCGAGACCuGcgGGGCCUcUugC- -5'
8838	3'	-61.1	NC_002484.1	+	29544	1.08	0.000423
	Target:  5'- uCGGCGCUCUGGACGCCCCGGAGAACGu -3' miRNA:   3'- -GCCGCGAGACCUGCGGGGCCUCUUGC- -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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