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
22413	3'	-57	NC_005056.1	+	20689	0.67	0.373816
	Target:  5'- cUGAUGGCagaGGaaGGGCggGCGuGGCCGu -3' miRNA:   3'- -ACUAUUGg--CCggUCCGa-UGCuCCGGU- -5'
22413	3'	-57	NC_005056.1	+	8647	0.67	0.391352
	Target:  5'- cGGU-GCUGGCguGGCUGCGGGaaaaucaGCCc -3' miRNA:   3'- aCUAuUGGCCGguCCGAUGCUC-------CGGu -5'
22413	3'	-57	NC_005056.1	+	21073	0.67	0.401747
	Target:  5'- gGAUAACCGG---GGCUuuGAGGCUg -3' miRNA:   3'- aCUAUUGGCCgguCCGAugCUCCGGu -5'
22413	3'	-57	NC_005056.1	+	7288	0.67	0.401747
	Target:  5'- cGGUAAUgCGGCCAGaacagguaaaGCUGCugauagcgaccgGAGGCCGu -3' miRNA:   3'- aCUAUUG-GCCGGUC----------CGAUG------------CUCCGGU- -5'
22413	3'	-57	NC_005056.1	+	11815	0.68	0.329442
	Target:  5'- aGGUAGCCGGgaaugucCCGGGUaAUGuucAGGCCAa -3' miRNA:   3'- aCUAUUGGCC-------GGUCCGaUGC---UCCGGU- -5'
22413	3'	-57	NC_005056.1	+	8893	0.7	0.241441
	Target:  5'- gGGUGACCGGCUccGGCgGCGGGGguuCCGg -3' miRNA:   3'- aCUAUUGGCCGGu-CCGaUGCUCC---GGU- -5'
22413	3'	-57	NC_005056.1	+	19736	1.08	0.000331
	Target:  5'- gUGAUAACCGGCCAGGCUACGAGGCCAu -3' miRNA:   3'- -ACUAUUGGCCGGUCCGAUGCUCCGGU- -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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