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
16642	5'	-50.2	NC_004156.1	+	9253	0.66	0.999213
	Target:  5'- uCCUCGUUcuGAGAuugaucAUCCUCGUugGCCUc -3' miRNA:   3'- cGGAGCAAacUUCU------UAGGGGCA--UGGA- -5'
16642	5'	-50.2	NC_004156.1	+	114469	0.67	0.997186
	Target:  5'- gGUCaUCcUUUGAAGAAUCCCUGcgAUCUg -3' miRNA:   3'- -CGG-AGcAAACUUCUUAGGGGCa-UGGA- -5'
16642	5'	-50.2	NC_004156.1	+	20477	0.68	0.995479
	Target:  5'- gGUCUC--UUGAAGAGUCCCaucaGUGCaCUc -3' miRNA:   3'- -CGGAGcaAACUUCUUAGGGg---CAUG-GA- -5'
16642	5'	-50.2	NC_004156.1	+	88769	0.68	0.99475
	Target:  5'- aGCCUUGUUggccaGAGAA-CUCUGUACCg -3' miRNA:   3'- -CGGAGCAAac---UUCUUaGGGGCAUGGa -5'
16642	5'	-50.2	NC_004156.1	+	213472	0.68	0.99475
	Target:  5'- aGUgUCGUUUGguGAggCCCUGUACa- -3' miRNA:   3'- -CGgAGCAAACuuCUuaGGGGCAUGga -5'
16642	5'	-50.2	NC_004156.1	+	107047	0.72	0.954053
	Target:  5'- aGCCUCGUgaaacGAGUCCCUcUGCCa -3' miRNA:   3'- -CGGAGCAaacuuCUUAGGGGcAUGGa -5'
16642	5'	-50.2	NC_004156.1	+	84623	0.73	0.925948
	Target:  5'- cGCCUUcUUUGAAGAcuAUCCaCCGUACg- -3' miRNA:   3'- -CGGAGcAAACUUCU--UAGG-GGCAUGga -5'
16642	5'	-50.2	NC_004156.1	+	92333	1.1	0.014791
	Target:  5'- uGCCUCGUUUGAAGAAUCCCCGUACCUc -3' miRNA:   3'- -CGGAGCAAACUUCUUAGGGGCAUGGA- -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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