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
18515	3'	-57.3	NC_004681.1	+	4182	0.66	0.729287
	Target:  5'- --aGGAAGcgacccAGcgCGGGGuuGGcGUGGGg -3' miRNA:   3'- cuaCCUUC------UCuaGCCCCucCC-CACCC- -5'
18515	3'	-57.3	NC_004681.1	+	7568	0.66	0.708822
	Target:  5'- cGGUGGAGGAcGGcCGGGGAGGccGUGa- -3' miRNA:   3'- -CUACCUUCU-CUaGCCCCUCCc-CACcc -5'
18515	3'	-57.3	NC_004681.1	+	33924	0.67	0.677631
	Target:  5'- -cUGGuAGGGA-CGGGGAauGGGGUGc- -3' miRNA:   3'- cuACCuUCUCUaGCCCCU--CCCCACcc -5'
18515	3'	-57.3	NC_004681.1	+	51779	0.67	0.646081
	Target:  5'- --cGGAAuccaccuguuGAGuUCGGGccauGGGGUGGGg -3' miRNA:   3'- cuaCCUU----------CUCuAGCCCcu--CCCCACCC- -5'
18515	3'	-57.3	NC_004681.1	+	2990	0.68	0.60389
	Target:  5'- --aGGAuguAGGGGUCGagcGGGAGGGG-GGc -3' miRNA:   3'- cuaCCU---UCUCUAGC---CCCUCCCCaCCc -5'
18515	3'	-57.3	NC_004681.1	+	63197	0.71	0.432755
	Target:  5'- --cGGcGGAGAUCGGGaaGAGGuucggcuucgcccGGUGGGa -3' miRNA:   3'- cuaCCuUCUCUAGCCC--CUCC-------------CCACCC- -5'
18515	3'	-57.3	NC_004681.1	+	63125	1.1	0.000946
	Target:  5'- aGAUGGAAGAGAUCGGGGAGGGGUGGGu -3' miRNA:   3'- -CUACCUUCUCUAGCCCCUCCCCACCC- -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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