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
1105	3'	-49.9	NC_000935.1	+	12643	0.66	0.85107
	Target:  5'- aAUAcCGCuGAGC-AGCCA-GCGCAa -3' miRNA:   3'- cUAUaGCGuUUCGuUCGGUuCGCGUg -5'
1105	3'	-49.9	NC_000935.1	+	18151	0.66	0.850139
	Target:  5'- uGGUAUgGCcggugcguuaaccGGAGCAAGCauuGGCGCGa -3' miRNA:   3'- -CUAUAgCG-------------UUUCGUUCGgu-UCGCGUg -5'
1105	3'	-49.9	NC_000935.1	+	34404	0.66	0.838755
	Target:  5'- ----gCGCAAaaagccaugaagauGGCAAcccuuGCCGAGCGCAg -3' miRNA:   3'- cuauaGCGUU--------------UCGUU-----CGGUUCGCGUg -5'
1105	3'	-49.9	NC_000935.1	+	10397	0.67	0.801387
	Target:  5'- -uUAUgCGC-AAGUuuGaCCGAGCGCACu -3' miRNA:   3'- cuAUA-GCGuUUCGuuC-GGUUCGCGUG- -5'
1105	3'	-49.9	NC_000935.1	+	7207	0.68	0.733783
	Target:  5'- uGAUAUCGCGcccgcAGCAgggccauuaugaaAGCCAGuGcCGCGCa -3' miRNA:   3'- -CUAUAGCGUu----UCGU-------------UCGGUU-C-GCGUG- -5'
1105	3'	-49.9	NC_000935.1	+	11745	0.7	0.627886
	Target:  5'- aAUAUgGCGAAG--AGCCuuAAGCGCGCg -3' miRNA:   3'- cUAUAgCGUUUCguUCGG--UUCGCGUG- -5'
1105	3'	-49.9	NC_000935.1	+	31429	1.1	0.001451
	Target:  5'- aGAUAUCGCAAAGCAAGCCAAGCGCACc -3' miRNA:   3'- -CUAUAGCGUUUCGUUCGGUUCGCGUG- -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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