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
27925	3'	-55.7	NC_005886.2	+	2399	0.66	0.601108
	Target:  5'- ---aGGCUGUGUcgcguccggGACGGCAGAuugaUCGCc -3' miRNA:   3'- cacaCCGACGCG---------UUGUCGUCU----AGCGc -5'
27925	3'	-55.7	NC_005886.2	+	37106	0.66	0.578758
	Target:  5'- ---cGGCagGCGUGACGGCAGGacUCGuCGg -3' miRNA:   3'- cacaCCGa-CGCGUUGUCGUCU--AGC-GC- -5'
27925	3'	-55.7	NC_005886.2	+	32016	0.67	0.5456
	Target:  5'- -gGU-GCUGCGCucGCAcCGGAUCGCa -3' miRNA:   3'- caCAcCGACGCGu-UGUcGUCUAGCGc -5'
27925	3'	-55.7	NC_005886.2	+	44922	0.68	0.501348
	Target:  5'- -cGUGGUucgaUGCGCGcagucgaucggauGC-GCAGAUUGCGg -3' miRNA:   3'- caCACCG----ACGCGU-------------UGuCGUCUAGCGC- -5'
27925	3'	-55.7	NC_005886.2	+	25763	0.7	0.365508
	Target:  5'- --aUGGCUGCGUucAACGGguGAcgaucacgcaUCGCGg -3' miRNA:   3'- cacACCGACGCG--UUGUCguCU----------AGCGC- -5'
27925	3'	-55.7	NC_005886.2	+	36525	0.74	0.212889
	Target:  5'- aUGUGGUgcacgacguUGCcCAguuuGCAGCAGAUCGCGg -3' miRNA:   3'- cACACCG---------ACGcGU----UGUCGUCUAGCGC- -5'
27925	3'	-55.7	NC_005886.2	+	13715	1.09	0.000598
	Target:  5'- gGUGUGGCUGCGCAACAGCAGAUCGCGg -3' miRNA:   3'- -CACACCGACGCGUUGUCGUCUAGCGC- -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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