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
10510	3'	-59.1	NC_002687.1	+	103455	0.66	0.934487
	Target:  5'- gUCGGcACCCGcguUGUUCCCGGcGucgacaucGGCUUUc -3' miRNA:   3'- -AGCC-UGGGUu--GCAAGGGCC-C--------CCGAAG- -5'
10510	3'	-59.1	NC_002687.1	+	78526	0.66	0.929783
	Target:  5'- -aGcACCCAGCGUU-CCGGGGaGCg-- -3' miRNA:   3'- agCcUGGGUUGCAAgGGCCCC-CGaag -5'
10510	3'	-59.1	NC_002687.1	+	304240	0.67	0.908916
	Target:  5'- aUCGGugUUGACuUUCUCGGGaauucucggcGGCUUCa -3' miRNA:   3'- -AGCCugGGUUGcAAGGGCCC----------CCGAAG- -5'
10510	3'	-59.1	NC_002687.1	+	87548	0.67	0.903191
	Target:  5'- gUUGGugcGCCCGACGUUgUggCGGGGGUUa- -3' miRNA:   3'- -AGCC---UGGGUUGCAAgG--GCCCCCGAag -5'
10510	3'	-59.1	NC_002687.1	+	223567	0.68	0.857665
	Target:  5'- uUCGGGCagcucgggCAGCGcggUCCCGGGGGa--- -3' miRNA:   3'- -AGCCUGg-------GUUGCa--AGGGCCCCCgaag -5'
10510	3'	-59.1	NC_002687.1	+	96846	0.71	0.697216
	Target:  5'- aCGcGGCCC-GCGUcgCUCGcGGGGCUUCc -3' miRNA:   3'- aGC-CUGGGuUGCAa-GGGC-CCCCGAAG- -5'
10510	3'	-59.1	NC_002687.1	+	159251	1.09	0.003615
	Target:  5'- aUCGGACCCAACGUUCCCGGGGGCUUCu -3' miRNA:   3'- -AGCCUGGGUUGCAAGGGCCCCCGAAG- -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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