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
23363	5'	-55.4	NC_005259.1	+	22279	0.66	0.802659
	Target:  5'- -cGCcgGGGC-CGAGGGUUUCCAcacGACGu -3' miRNA:   3'- gaCG--CUUGcGCUCCCAGAGGUa--CUGC- -5'
23363	5'	-55.4	NC_005259.1	+	40006	0.66	0.802659
	Target:  5'- -cGcCGAGCaUGAGGGUCUgaCCggGACGu -3' miRNA:   3'- gaC-GCUUGcGCUCCCAGA--GGuaCUGC- -5'
23363	5'	-55.4	NC_005259.1	+	64936	0.66	0.783596
	Target:  5'- gUGCcAGCGCGAGGGUggCCGgguugucGAUGg -3' miRNA:   3'- gACGcUUGCGCUCCCAgaGGUa------CUGC- -5'
23363	5'	-55.4	NC_005259.1	+	7197	0.67	0.723136
	Target:  5'- cCUGCGGACGCaccGGGcugcgguggaUCUgCGUGAUGa -3' miRNA:   3'- -GACGCUUGCGcu-CCC----------AGAgGUACUGC- -5'
23363	5'	-55.4	NC_005259.1	+	51151	0.68	0.691594
	Target:  5'- --aUGAGCGCGuucGGGUUgaCCGUGGCGa -3' miRNA:   3'- gacGCUUGCGCu--CCCAGa-GGUACUGC- -5'
23363	5'	-55.4	NC_005259.1	+	14152	0.69	0.605801
	Target:  5'- gUGCGAGCGCGucguguGGaUCUCgCcgGGCGg -3' miRNA:   3'- gACGCUUGCGCu-----CCcAGAG-GuaCUGC- -5'
23363	5'	-55.4	NC_005259.1	+	6646	0.73	0.395679
	Target:  5'- -cGUGAcgacACGguCGAGGGUgUCCGUGACGc -3' miRNA:   3'- gaCGCU----UGC--GCUCCCAgAGGUACUGC- -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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