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
13544	3'	-49.6	NC_003444.1	+	13027	0.66	0.911683
	Target:  5'- gGCUGGAcAUCGGUGcgCaUCggUGCCGGu -3' miRNA:   3'- -UGGCUU-UAGCCACaaG-AGaaGUGGCC- -5'
13544	3'	-49.6	NC_003444.1	+	11433	0.67	0.889991
	Target:  5'- cGCCGGAuaaGGUGUguaUCcccgCGCCGGu -3' miRNA:   3'- -UGGCUUuagCCACAag-AGaa--GUGGCC- -5'
13544	3'	-49.6	NC_003444.1	+	7548	0.67	0.857007
	Target:  5'- uAUCGucAUCGGUGUUCacCUUuuuauuaacgCGCCGGa -3' miRNA:   3'- -UGGCuuUAGCCACAAGa-GAA----------GUGGCC- -5'
13544	3'	-49.6	NC_003444.1	+	25393	0.7	0.713286
	Target:  5'- gGCUGGAGUU-GUGUUCUCUUuaCGCCGu -3' miRNA:   3'- -UGGCUUUAGcCACAAGAGAA--GUGGCc -5'
13544	3'	-49.6	NC_003444.1	+	36453	0.72	0.632568
	Target:  5'- cGCCGGAAUCGGUacguaaacuGUUCgcguaCUUCcgcaACCGGu -3' miRNA:   3'- -UGGCUUUAGCCA---------CAAGa----GAAG----UGGCC- -5'
13544	3'	-49.6	NC_003444.1	+	4778	0.73	0.54042
	Target:  5'- uCCGAAGUUGGUGUUCU----GCUGGg -3' miRNA:   3'- uGGCUUUAGCCACAAGAgaagUGGCC- -5'
13544	3'	-49.6	NC_003444.1	+	4877	0.97	0.018459
	Target:  5'- uACCGAAAUCGGUGUcUUCUUCACCGGc -3' miRNA:   3'- -UGGCUUUAGCCACAaGAGAAGUGGCC- -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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