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
12314	3'	-63.3	NC_003323.1	+	1867	1.09	1.1e-05
	Target:  5'- gCCCCUGCCCUCUCUGCCAGGACCCCGc -3' miRNA:   3'- -GGGGACGGGAGAGACGGUCCUGGGGC- -5'
12314	3'	-63.3	NC_003323.1	+	2492	0.69	0.035854
	Target:  5'- cCUCCagGCCCUgaCUGaccugguuuCCAGGGCCCUGg -3' miRNA:   3'- -GGGGa-CGGGAgaGAC---------GGUCCUGGGGC- -5'
12314	3'	-63.3	NC_003323.1	+	3786	0.67	0.052479
	Target:  5'- cCCCCUGCCUcuUCUCggaCGGGGCUaCCu -3' miRNA:   3'- -GGGGACGGG--AGAGacgGUCCUGG-GGc -5'
12314	3'	-63.3	NC_003323.1	+	1119	0.67	0.059162
	Target:  5'- cUCCCUGUCCUUcacccccaCGGGGCCCCa -3' miRNA:   3'- -GGGGACGGGAGagacg---GUCCUGGGGc -5'
12314	3'	-63.3	NC_003323.1	+	291	0.66	0.067507
	Target:  5'- aCCCCU-CCCUCg--GCCGuGGaccaGCCCUGg -3' miRNA:   3'- -GGGGAcGGGAGagaCGGU-CC----UGGGGC- -5'
12314	3'	-63.3	NC_003323.1	+	8507	0.66	0.067507
	Target:  5'- aCCCCU-CCCUCg--GCCGuGGaccaGCCCUGg -3' miRNA:   3'- -GGGGAcGGGAGagaCGGU-CC----UGGGGC- -5'
12314	3'	-63.3	NC_003323.1	+	4809	0.66	0.069655
	Target:  5'- gCCCCUGCCUuccaUCUCUGaaaaCAcacucccACCCCGu -3' miRNA:   3'- -GGGGACGGG----AGAGACg---GUcc-----UGGGGC- -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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