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
22344	3'	-55	NC_005045.1	+	41325	0.66	0.643939
	Target:  5'- gGUgGUAGGGUcaaucaguGGGUGUucgcacagcacagcgGGCGCcGGGg -3' miRNA:   3'- gCAgCAUUCCG--------UCCAUA---------------CCGCGuCCC- -5'
22344	3'	-55	NC_005045.1	+	34822	0.66	0.639467
	Target:  5'- ---gGUGGcGCGGGc--GGCGCAGGGg -3' miRNA:   3'- gcagCAUUcCGUCCauaCCGCGUCCC- -5'
22344	3'	-55	NC_005045.1	+	32215	0.68	0.550647
	Target:  5'- -aUCGU--GGCGGGUGcucuUGGCGCuggcguGGGu -3' miRNA:   3'- gcAGCAuuCCGUCCAU----ACCGCGu-----CCC- -5'
22344	3'	-55	NC_005045.1	+	32629	0.69	0.46493
	Target:  5'- ----cUGGGGCAGcguaccgcguuccGUGUGGUGCAGGGc -3' miRNA:   3'- gcagcAUUCCGUC-------------CAUACCGCGUCCC- -5'
22344	3'	-55	NC_005045.1	+	17734	0.69	0.463914
	Target:  5'- aGUCGUGAGGCAGGUAgcccuugaccucGGCGg---- -3' miRNA:   3'- gCAGCAUUCCGUCCAUa-----------CCGCguccc -5'
22344	3'	-55	NC_005045.1	+	10832	0.73	0.304364
	Target:  5'- uCGUCGauguGGGCguugAGGUA-GGCGCAGGu -3' miRNA:   3'- -GCAGCau--UCCG----UCCAUaCCGCGUCCc -5'
22344	3'	-55	NC_005045.1	+	24070	1.1	0.000671
	Target:  5'- gCGUCGUAAGGCAGGUAUGGCGCAGGGu -3' miRNA:   3'- -GCAGCAUUCCGUCCAUACCGCGUCCC- -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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