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
30534	3'	-52.7	NC_006548.1	+	4502	0.66	0.747435
	Target:  5'- gGCAACAugauGAUCGCggcgaugaaUCUGg-CGGUGCAu -3' miRNA:   3'- -CGUUGUu---CUGGUG---------AGACagGCCACGU- -5'
30534	3'	-52.7	NC_006548.1	+	36387	0.67	0.702926
	Target:  5'- cGCAGCGAGgauGCCugUC--UCUGGcUGCAg -3' miRNA:   3'- -CGUUGUUC---UGGugAGacAGGCC-ACGU- -5'
30534	3'	-52.7	NC_006548.1	+	22562	0.67	0.691576
	Target:  5'- uGCGGCAGGugcaGCCGCUUUGUCCuugucguuacuGGauuUGCGg -3' miRNA:   3'- -CGUUGUUC----UGGUGAGACAGG-----------CC---ACGU- -5'
30534	3'	-52.7	NC_006548.1	+	7210	0.69	0.576624
	Target:  5'- aGCGACAGGcCCAgCUCUGcCgCGGcUGCu -3' miRNA:   3'- -CGUUGUUCuGGU-GAGACaG-GCC-ACGu -5'
30534	3'	-52.7	NC_006548.1	+	38253	0.7	0.52035
	Target:  5'- uCGGCAAgcuGACCGCUCUGUCUgagcgGGUGg- -3' miRNA:   3'- cGUUGUU---CUGGUGAGACAGG-----CCACgu -5'
30534	3'	-52.7	NC_006548.1	+	21725	0.76	0.223387
	Target:  5'- gGCAGCAccgaAGACCACggcCUGgacgcgCCGGUGCc -3' miRNA:   3'- -CGUUGU----UCUGGUGa--GACa-----GGCCACGu -5'
30534	3'	-52.7	NC_006548.1	+	21899	1.11	0.000786
	Target:  5'- gGCAACAAGACCACUCUGUCCGGUGCAg -3' miRNA:   3'- -CGUUGUUCUGGUGAGACAGGCCACGU- -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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