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
6305	5'	-54.1	NC_001844.1	+	22854	0.66	0.938325
	Target:  5'- uUgCAUuuACUCgucCGGGGGCGUacuuGGGGCu -3' miRNA:   3'- cAgGUAu-UGAGa--GCCCUCGCA----CCUCG- -5'
6305	5'	-54.1	NC_001844.1	+	140957	0.67	0.910983
	Target:  5'- -aCCAUcuucAGCaUCUCGGcGAGCcccGGAGCg -3' miRNA:   3'- caGGUA----UUG-AGAGCC-CUCGca-CCUCG- -5'
6305	5'	-54.1	NC_001844.1	+	120238	0.67	0.910983
	Target:  5'- aGUCUAUGcGCUggCuGGAGCGUGGGGa -3' miRNA:   3'- -CAGGUAU-UGAgaGcCCUCGCACCUCg -5'
6305	5'	-54.1	NC_001844.1	+	43999	0.68	0.904778
	Target:  5'- uUCCG--GCUCUUuuugGGGAGC-UGGGGUg -3' miRNA:   3'- cAGGUauUGAGAG----CCCUCGcACCUCG- -5'
6305	5'	-54.1	NC_001844.1	+	113292	0.69	0.826736
	Target:  5'- aGUCCGacgaugAGCUUgagaucgacggacCGGGGGaCGUGGAGCu -3' miRNA:   3'- -CAGGUa-----UUGAGa------------GCCCUC-GCACCUCG- -5'
6305	5'	-54.1	NC_001844.1	+	137764	0.71	0.737257
	Target:  5'- -cCCGUAcCugUCUCGGGGGCcG-GGAGCg -3' miRNA:   3'- caGGUAUuG--AGAGCCCUCG-CaCCUCG- -5'
6305	5'	-54.1	NC_001844.1	+	121477	1.11	0.003074
	Target:  5'- aGUCCAUAACUCUCGGGAGCGUGGAGCc -3' miRNA:   3'- -CAGGUAUUGAGAGCCCUCGCACCUCG- -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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