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
20845	3'	-61.8	NC_004689.1	+	36896	0.66	0.425161
	Target:  5'- gGCCUCGCuGGccUGCCccGGUC-GCCCc-- -3' miRNA:   3'- aCGGAGCG-CC--ACGG--CCAGaCGGGuag -5'
20845	3'	-61.8	NC_004689.1	+	15736	0.66	0.416176
	Target:  5'- cGCCUgccaGCGGUGCCuuGGgcuugcucUCUG-CCAUCg -3' miRNA:   3'- aCGGAg---CGCCACGG--CC--------AGACgGGUAG- -5'
20845	3'	-61.8	NC_004689.1	+	52428	0.67	0.368076
	Target:  5'- aGCCUgCGCGGgugccuuuuucacaGCCGGUgcagCUGCCUuuuUCg -3' miRNA:   3'- aCGGA-GCGCCa-------------CGGCCA----GACGGGu--AG- -5'
20845	3'	-61.8	NC_004689.1	+	17104	0.67	0.356662
	Target:  5'- gGCCcUGCGGUgagGCCGGUCUGagugaCGUUg -3' miRNA:   3'- aCGGaGCGCCA---CGGCCAGACgg---GUAG- -5'
20845	3'	-61.8	NC_004689.1	+	12242	0.68	0.333051
	Target:  5'- cGCUugUCGUaGUGCCgcaGGUCguaGCCCAUCu -3' miRNA:   3'- aCGG--AGCGcCACGG---CCAGa--CGGGUAG- -5'
20845	3'	-61.8	NC_004689.1	+	70412	0.7	0.232393
	Target:  5'- gGCCUCG-GGUGCCacgaccauGGUCgGCUCAUg -3' miRNA:   3'- aCGGAGCgCCACGG--------CCAGaCGGGUAg -5'
20845	3'	-61.8	NC_004689.1	+	60962	0.7	0.230668
	Target:  5'- gGCCUCGguguacccccacucCGGcGCUGGUgCUGCCCAg- -3' miRNA:   3'- aCGGAGC--------------GCCaCGGCCA-GACGGGUag -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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