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
26059	3'	-53.9	NC_005342.2	+	17760	0.66	0.709019
	Target:  5'- --gCUCGGgcUCGACAAgguaggcgcAGCCGUGAc -3' miRNA:   3'- gagGAGCCgaAGCUGUU---------UCGGCACUa -5'
26059	3'	-53.9	NC_005342.2	+	20349	0.66	0.697929
	Target:  5'- -aCCgcgacCGGCUUCGugAAcGCCGUcGAa -3' miRNA:   3'- gaGGa----GCCGAAGCugUUuCGGCA-CUa -5'
26059	3'	-53.9	NC_005342.2	+	25617	0.67	0.675559
	Target:  5'- uUCgUCGGCUUCcucguGGCGAAGuuGUGc- -3' miRNA:   3'- gAGgAGCCGAAG-----CUGUUUCggCACua -5'
26059	3'	-53.9	NC_005342.2	+	45136	0.67	0.664303
	Target:  5'- --aCUCGGUUUCGGCGgcGCCGa--- -3' miRNA:   3'- gagGAGCCGAAGCUGUuuCGGCacua -5'
26059	3'	-53.9	NC_005342.2	+	31019	0.68	0.585238
	Target:  5'- uUUCUCGGCUguaccgacgUCGACAaccauaAAGCCGUa-- -3' miRNA:   3'- gAGGAGCCGA---------AGCUGU------UUCGGCAcua -5'
26059	3'	-53.9	NC_005342.2	+	5669	0.7	0.466006
	Target:  5'- cCUCCU-GGCaaCGACGcggauaAGGCCGUGAUg -3' miRNA:   3'- -GAGGAgCCGaaGCUGU------UUCGGCACUA- -5'
26059	3'	-53.9	NC_005342.2	+	32329	1.05	0.001928
	Target:  5'- gCUCCUCGGCUUCGACAAAGCCGUGAUc -3' miRNA:   3'- -GAGGAGCCGAAGCUGUUUCGGCACUA- -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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