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
1313	3'	-55.3	NC_001331.1	+	915	0.66	0.184073
	Target:  5'- uGCCGGccuucGCCGGGGUGAUcgacaccagcgcgGUGGAaucGGCg -3' miRNA:   3'- -UGGCUac---CGGUCCCGCUA-------------UACUU---CCG- -5'
1313	3'	-55.3	NC_001331.1	+	352	0.66	0.167879
	Target:  5'- gGCCGG-GGCUuGGGCGGUcgGcgccaucGGCu -3' miRNA:   3'- -UGGCUaCCGGuCCCGCUAuaCuu-----CCG- -5'
1313	3'	-55.3	NC_001331.1	+	4134	0.66	0.181186
	Target:  5'- -aCGAUGGUCAGcGGCGAcuggccccuggccgGUGcgucugcgGAGGCg -3' miRNA:   3'- ugGCUACCGGUC-CCGCUa-------------UAC--------UUCCG- -5'
1313	3'	-55.3	NC_001331.1	+	6889	0.67	0.14764
	Target:  5'- gACCGGaucGGCCAcggugcGGGCGGcuUGGaucAGGCa -3' miRNA:   3'- -UGGCUa--CCGGU------CCCGCUauACU---UCCG- -5'
1313	3'	-55.3	NC_001331.1	+	3539	0.75	0.032478
	Target:  5'- uGCCGGUGGCCGuGGacuGGUA-GAGGGCg -3' miRNA:   3'- -UGGCUACCGGUcCCg--CUAUaCUUCCG- -5'
1313	3'	-55.3	NC_001331.1	+	4280	0.76	0.028984
	Target:  5'- cGCCGccGGCCGGGagcgcaaggcaugaGCGAUAggccGAAGGCg -3' miRNA:   3'- -UGGCuaCCGGUCC--------------CGCUAUa---CUUCCG- -5'
1313	3'	-55.3	NC_001331.1	+	964	1.1	3.6e-05
	Target:  5'- cACCGAUGGCCAGGGCGAUAUGAAGGCc -3' miRNA:   3'- -UGGCUACCGGUCCCGCUAUACUUCCG- -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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