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
31612	5'	-55.3	NC_006879.1	+	17588	0.66	0.567299
	Target:  5'- cGCCCgcgcCACCgACACCUacuucagCUUGGGAAa -3' miRNA:   3'- -CGGGa---GUGGgUGUGGAga-----GAGUCUUU- -5'
31612	5'	-55.3	NC_006879.1	+	28671	0.66	0.555965
	Target:  5'- uGUCCUCACCCACAauuuucauCUUUUCaUAGAu- -3' miRNA:   3'- -CGGGAGUGGGUGU--------GGAGAGaGUCUuu -5'
31612	5'	-55.3	NC_006879.1	+	22179	0.66	0.544696
	Target:  5'- uGCCUUCGCCCuCGCUgucggagacaaUCUC-CGGGGAu -3' miRNA:   3'- -CGGGAGUGGGuGUGG-----------AGAGaGUCUUU- -5'
31612	5'	-55.3	NC_006879.1	+	10913	0.66	0.511374
	Target:  5'- cCCCUCuCCUGCACCacgaugCUCUgCAGGAu -3' miRNA:   3'- cGGGAGuGGGUGUGGa-----GAGA-GUCUUu -5'
31612	5'	-55.3	NC_006879.1	+	5391	0.67	0.489634
	Target:  5'- aGCCUggACCCGaGCCUUugUCUCGGAGu -3' miRNA:   3'- -CGGGagUGGGUgUGGAG--AGAGUCUUu -5'
31612	5'	-55.3	NC_006879.1	+	8210	0.68	0.427235
	Target:  5'- cGUCgUCGCCCACGCCagcagUCUC-CGGGc- -3' miRNA:   3'- -CGGgAGUGGGUGUGG-----AGAGaGUCUuu -5'
31612	5'	-55.3	NC_006879.1	+	6820	1.09	0.000481
	Target:  5'- cGCCCUCACCCACACCUCUCUCAGAAAg -3' miRNA:   3'- -CGGGAGUGGGUGUGGAGAGAGUCUUU- -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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