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
6213	3'	-52.2	NC_001844.1	+	141633	0.66	0.97933
	Target:  5'- uUGgGUGGCaGCGcuugcGCUUAgAGGCCCg -3' miRNA:   3'- -ACaCACCG-CGCua---CGAAUaUUCGGGg -5'
6213	3'	-52.2	NC_001844.1	+	80713	0.67	0.968463
	Target:  5'- aGUGgcaGCGCGcgGCUcGUAAGCagcuguaaacCCCa -3' miRNA:   3'- aCACac-CGCGCuaCGAaUAUUCG----------GGG- -5'
6213	3'	-52.2	NC_001844.1	+	79955	0.67	0.952812
	Target:  5'- --gGUGGCGCGGgucgcugggGCUgGUGGgggcaauuucuucuGCCCCa -3' miRNA:   3'- acaCACCGCGCUa--------CGAaUAUU--------------CGGGG- -5'
6213	3'	-52.2	NC_001844.1	+	124707	0.68	0.929983
	Target:  5'- cUGUG-GGCGUG-UGCUUAUaAAGCuacgaauCCCg -3' miRNA:   3'- -ACACaCCGCGCuACGAAUA-UUCG-------GGG- -5'
6213	3'	-52.2	NC_001844.1	+	143468	0.72	0.776476
	Target:  5'- gGUGUGGCcccuCGG-GCggcAUGGGCCCCa -3' miRNA:   3'- aCACACCGc---GCUaCGaa-UAUUCGGGG- -5'
6213	3'	-52.2	NC_001844.1	+	5752	0.76	0.590048
	Target:  5'- aGUG-GGCGCG--GCUUGUAAGUCUCu -3' miRNA:   3'- aCACaCCGCGCuaCGAAUAUUCGGGG- -5'
6213	3'	-52.2	NC_001844.1	+	70409	1.13	0.003042
	Target:  5'- cUGUGUGGCGCGAUGCUUAUAAGCCCCa -3' miRNA:   3'- -ACACACCGCGCUACGAAUAUUCGGGG- -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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