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
32794	5'	-49.5	NC_007346.1	+	277468	0.66	0.999983
	Target:  5'- uGGUAUAcaacacccUCUCGUgcaaCUCGGUCGgucguguacGCUUGCc -3' miRNA:   3'- -UCAUAU--------AGGGUA----GAGCCAGU---------CGAACG- -5'
32794	5'	-49.5	NC_007346.1	+	301505	0.69	0.999155
	Target:  5'- --aGUAUUUCAUCUUGGUgAGCUuUGUa -3' miRNA:   3'- ucaUAUAGGGUAGAGCCAgUCGA-ACG- -5'
32794	5'	-49.5	NC_007346.1	+	265209	0.69	0.998977
	Target:  5'- --cGUGUCCCGaCgCGGUCGGCgUGUc -3' miRNA:   3'- ucaUAUAGGGUaGaGCCAGUCGaACG- -5'
32794	5'	-49.5	NC_007346.1	+	159985	0.7	0.998522
	Target:  5'- uAGUGUGUCCauaauaGGUCuacuGCUUGCa -3' miRNA:   3'- -UCAUAUAGGguagagCCAGu---CGAACG- -5'
32794	5'	-49.5	NC_007346.1	+	364307	0.71	0.995384
	Target:  5'- cGGUGUAUUCaauaAUCUCGGUacaUAGgUUGCu -3' miRNA:   3'- -UCAUAUAGGg---UAGAGCCA---GUCgAACG- -5'
32794	5'	-49.5	NC_007346.1	+	242180	0.73	0.979132
	Target:  5'- cGUAUAcCCCAUgUCGGUgacgaAGUUUGCg -3' miRNA:   3'- uCAUAUaGGGUAgAGCCAg----UCGAACG- -5'
32794	5'	-49.5	NC_007346.1	+	23796	0.8	0.781819
	Target:  5'- cAGUAUAUUCCAUCUCGGUCGauccacauaaUUGCa -3' miRNA:   3'- -UCAUAUAGGGUAGAGCCAGUcg--------AACG- -5'
32794	5'	-49.5	NC_007346.1	+	261539	1.14	0.016328
	Target:  5'- uAGUAUAUCCCAUCUCGGUCAGCUUGCg -3' miRNA:   3'- -UCAUAUAGGGUAGAGCCAGUCGAACG- -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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