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
10261	5'	-44.3	NC_002686.1	+	72815	0.66	0.999995
	Target:  5'- ---aGGAUAuGAUACGCgggUAGACUgauagACa -3' miRNA:   3'- cacaCCUAU-CUGUGCGa--AUUUGAa----UG- -5'
10261	5'	-44.3	NC_002686.1	+	20680	0.66	0.999989
	Target:  5'- -gGUGGAUAGuC-CGCauUUAGugUUGCc -3' miRNA:   3'- caCACCUAUCuGuGCG--AAUUugAAUG- -5'
10261	5'	-44.3	NC_002686.1	+	17879	0.68	0.999777
	Target:  5'- --aUGGuuuuUAGAUAUGCUU-GACUUGCg -3' miRNA:   3'- cacACCu---AUCUGUGCGAAuUUGAAUG- -5'
10261	5'	-44.3	NC_002686.1	+	106489	0.69	0.999457
	Target:  5'- aGUGUGGGUAGGcCAUGguggcauaagcccgcCUUAAACuUUGCa -3' miRNA:   3'- -CACACCUAUCU-GUGC---------------GAAUUUG-AAUG- -5'
10261	5'	-44.3	NC_002686.1	+	121666	0.69	0.999457
	Target:  5'- aGUGUGGGUAGGcCAUGguggcauaagcccgcCUUAAACuUUGCa -3' miRNA:   3'- -CACACCUAUCU-GUGC---------------GAAUUUG-AAUG- -5'
10261	5'	-44.3	NC_002686.1	+	43996	0.81	0.751585
	Target:  5'- uGUGcGGAUAGACACGCUUAcguuagguAACUUGu -3' miRNA:   3'- -CACaCCUAUCUGUGCGAAU--------UUGAAUg -5'
10261	5'	-44.3	NC_002686.1	+	43879	1.12	0.019737
	Target:  5'- uGUGUGGAUAGACACGCUUAAACUUACa -3' miRNA:   3'- -CACACCUAUCUGUGCGAAUUUGAAUG- -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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