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
17369	3'	-46.7	NC_004367.1	+	9102	0.66	0.99985
	Target:  5'- -----aUGCCGCCGcaaAACAGCCgUUCc -3' miRNA:   3'- gauauaAUGGUGGCac-UUGUCGG-AAG- -5'
17369	3'	-46.7	NC_004367.1	+	34159	0.66	0.99985
	Target:  5'- uCUGUGggAUCAUUGUGAGUAGCUUUUc -3' miRNA:   3'- -GAUAUaaUGGUGGCACUUGUCGGAAG- -5'
17369	3'	-46.7	NC_004367.1	+	8001	0.66	0.99985
	Target:  5'- cCUAUGUcGCCACC-UGGAucagucCAGCCUc- -3' miRNA:   3'- -GAUAUAaUGGUGGcACUU------GUCGGAag -5'
17369	3'	-46.7	NC_004367.1	+	52971	0.66	0.999801
	Target:  5'- aUGUAUUACCAgCGUGAgccauuuACAGUg--- -3' miRNA:   3'- gAUAUAAUGGUgGCACU-------UGUCGgaag -5'
17369	3'	-46.7	NC_004367.1	+	27247	0.69	0.997859
	Target:  5'- -cGUGUcAUUACCGUGu-CAGCCUUUc -3' miRNA:   3'- gaUAUAaUGGUGGCACuuGUCGGAAG- -5'
17369	3'	-46.7	NC_004367.1	+	96328	0.7	0.994965
	Target:  5'- -gAUAgc-CCGCCGUaGAGCGGCCg-- -3' miRNA:   3'- gaUAUaauGGUGGCA-CUUGUCGGaag -5'
17369	3'	-46.7	NC_004367.1	+	101165	0.7	0.994113
	Target:  5'- ------gGCCGCCGc-GGCGGCCUUCc -3' miRNA:   3'- gauauaaUGGUGGCacUUGUCGGAAG- -5'
17369	3'	-46.7	NC_004367.1	+	102924	1.12	0.013531
	Target:  5'- cCUAUAUUACCACCGUGAACAGCCUUCa -3' miRNA:   3'- -GAUAUAAUGGUGGCACUUGUCGGAAG- -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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