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
6299	5'	-53.2	NC_001844.1	+	12913	0.66	0.953783
	Target:  5'- -uGCUGCgucGCUugCauguGCGGCgGCUACg -3' miRNA:   3'- guCGACGa--UGAugG----UGUCGaCGAUGa -5'
6299	5'	-53.2	NC_001844.1	+	88814	0.66	0.945008
	Target:  5'- aCAGCgGCUugUGCCucCAcGC-GCUGCg -3' miRNA:   3'- -GUCGaCGAugAUGGu-GU-CGaCGAUGa -5'
6299	5'	-53.2	NC_001844.1	+	49030	0.66	0.945008
	Target:  5'- -cGUgGCUACUGCaCACGGUgaaGCUGCc -3' miRNA:   3'- guCGaCGAUGAUG-GUGUCGa--CGAUGa -5'
6299	5'	-53.2	NC_001844.1	+	40649	0.68	0.899547
	Target:  5'- gGGCUcGCUucuaGCcGCCGCAGCUugcgugGCUGCa -3' miRNA:   3'- gUCGA-CGA----UGaUGGUGUCGA------CGAUGa -5'
6299	5'	-53.2	NC_001844.1	+	65049	0.68	0.892702
	Target:  5'- aGGCUGUUACUucaGCAGCUGUuuUGCc -3' miRNA:   3'- gUCGACGAUGAuggUGUCGACG--AUGa -5'
6299	5'	-53.2	NC_001844.1	+	114455	0.68	0.885607
	Target:  5'- aGGCccugGCUACcAUCGCAGCccGCUGCa -3' miRNA:   3'- gUCGa---CGAUGaUGGUGUCGa-CGAUGa -5'
6299	5'	-53.2	NC_001844.1	+	97517	0.7	0.811468
	Target:  5'- --aCUGCUugUacaaaGCCAUAGCUGCUAg- -3' miRNA:   3'- gucGACGAugA-----UGGUGUCGACGAUga -5'
6299	5'	-53.2	NC_001844.1	+	39748	0.71	0.72307
	Target:  5'- --uCUGCU-UUGCCGCAGCUGuCUGCUu -3' miRNA:   3'- gucGACGAuGAUGGUGUCGAC-GAUGA- -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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