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
31896	3'	-53.3	NC_006938.1	+	59504	0.67	0.81887
	Target:  5'- -cCGGGUCCGgcggCGCCAcUCGAaacggaggcaagagaGUGCUg -3' miRNA:   3'- cuGCUCAGGCaa--GUGGU-AGCU---------------CACGA- -5'
31896	3'	-53.3	NC_006938.1	+	49992	0.67	0.776244
	Target:  5'- -uCGGGUCCGUUCACC-UCGAc---- -3' miRNA:   3'- cuGCUCAGGCAAGUGGuAGCUcacga -5'
31896	3'	-53.3	NC_006938.1	+	58356	0.68	0.74546
	Target:  5'- gGAUGAGUCCGUUgagaguguaggUGCCAUUG-GUGUUu -3' miRNA:   3'- -CUGCUCAGGCAA-----------GUGGUAGCuCACGA- -5'
31896	3'	-53.3	NC_006938.1	+	16406	0.69	0.702852
	Target:  5'- uGGCGAGcUCCGa--GCCGgagagCGGGUGCUu -3' miRNA:   3'- -CUGCUC-AGGCaagUGGUa----GCUCACGA- -5'
31896	3'	-53.3	NC_006938.1	+	24700	0.7	0.615002
	Target:  5'- -uCGAG-CCGUUCugUccCGAGUGCUg -3' miRNA:   3'- cuGCUCaGGCAAGugGuaGCUCACGA- -5'
31896	3'	-53.3	NC_006938.1	+	24162	0.75	0.371554
	Target:  5'- cGACGuGGUCCGUgugACCAUgCGAGUGCc -3' miRNA:   3'- -CUGC-UCAGGCAag-UGGUA-GCUCACGa -5'
31896	3'	-53.3	NC_006938.1	+	53961	1.09	0.002092
	Target:  5'- aGACGAGUCCGUUCACCAUCGAGUGCUg -3' miRNA:   3'- -CUGCUCAGGCAAGUGGUAGCUCACGA- -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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