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
30691	3'	-52.2	NC_006552.1	+	3576	0.67	0.85537
	Target:  5'- -gGGACgGCAACUGccUGAuCUGGAu- -3' miRNA:   3'- caCCUGgCGUUGACaaGCU-GACCUug -5'
30691	3'	-52.2	NC_006552.1	+	27032	0.67	0.846756
	Target:  5'- cUGG-CCGCGguaGCUGUUgGuGCUGGGAa -3' miRNA:   3'- cACCuGGCGU---UGACAAgC-UGACCUUg -5'
30691	3'	-52.2	NC_006552.1	+	15574	0.68	0.800396
	Target:  5'- -gGGACCGCGAag--UCGAuccgcuCUGGGACc -3' miRNA:   3'- caCCUGGCGUUgacaAGCU------GACCUUG- -5'
30691	3'	-52.2	NC_006552.1	+	7067	0.68	0.780507
	Target:  5'- aGUGGAagaCCGCAgccgACUGcaUCGACUGGucguACc -3' miRNA:   3'- -CACCU---GGCGU----UGACa-AGCUGACCu---UG- -5'
30691	3'	-52.2	NC_006552.1	+	37448	0.69	0.748462
	Target:  5'- aUGGugUGCGGCgugagacgcggcuUGgaUGGCUGGAACa -3' miRNA:   3'- cACCugGCGUUG-------------ACaaGCUGACCUUG- -5'
30691	3'	-52.2	NC_006552.1	+	29767	0.69	0.718501
	Target:  5'- cUGGGCCGCAGCcuucgcgucuugcgcGUUCGGCUGcuGCu -3' miRNA:   3'- cACCUGGCGUUGa--------------CAAGCUGACcuUG- -5'
30691	3'	-52.2	NC_006552.1	+	2820	1.09	0.002346
	Target:  5'- aGUGGACCGCAACUGUUCGACUGGAACc -3' miRNA:   3'- -CACCUGGCGUUGACAAGCUGACCUUG- -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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