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
22322	5'	-55.7	NC_005045.1	+	13530	0.66	0.608345
	Target:  5'- aAGGGCgUGCGcGAcaucaUGGcCGAcgCUGCCCGc -3' miRNA:   3'- -UCCUGgACGC-CU-----ACU-GCUa-GAUGGGC- -5'
22322	5'	-55.7	NC_005045.1	+	38227	0.66	0.597253
	Target:  5'- uGGGCCUGCuacAUGAgcUGGUCUGCaCCGc -3' miRNA:   3'- uCCUGGACGcc-UACU--GCUAGAUG-GGC- -5'
22322	5'	-55.7	NC_005045.1	+	23110	0.68	0.51031
	Target:  5'- uGGGCCUGCGcGGccugcUGACGcugCUGCuCCGc -3' miRNA:   3'- uCCUGGACGC-CU-----ACUGCua-GAUG-GGC- -5'
22322	5'	-55.7	NC_005045.1	+	24713	0.71	0.364643
	Target:  5'- -cGACCUGgGcGAUG-CGGUCUACuCCGa -3' miRNA:   3'- ucCUGGACgC-CUACuGCUAGAUG-GGC- -5'
22322	5'	-55.7	NC_005045.1	+	135	0.73	0.27058
	Target:  5'- cGGGAgugucaacCCUGCGG-UGGCGuggCUGCCCa -3' miRNA:   3'- -UCCU--------GGACGCCuACUGCua-GAUGGGc -5'
22322	5'	-55.7	NC_005045.1	+	42198	0.73	0.27058
	Target:  5'- cGGGAgugucaacCCUGCGG-UGGCGuggCUGCCCa -3' miRNA:   3'- -UCCU--------GGACGCCuACUGCua-GAUGGGc -5'
22322	5'	-55.7	NC_005045.1	+	15535	1.08	0.00079
	Target:  5'- aAGGACCUGCGGAUGACGAUCUACCCGu -3' miRNA:   3'- -UCCUGGACGCCUACUGCUAGAUGGGC- -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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