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
12591	5'	-58	NC_003345.1	+	11835	0.66	0.696122
	Target:  5'- uGACcucuACGGCGACCgUUGCCgGUGg -3' miRNA:   3'- gCUGac--UGCUGCUGGgGACGGgCAUa -5'
12591	5'	-58	NC_003345.1	+	73316	0.66	0.682607
	Target:  5'- cCGAUUcGACGGCGAaccucgucguggaaCCCCUGUCCc--- -3' miRNA:   3'- -GCUGA-CUGCUGCU--------------GGGGACGGGcaua -5'
12591	5'	-58	NC_003345.1	+	22091	0.66	0.664824
	Target:  5'- aCGACgagaACGGCGACCCCguugacGaCCCGg-- -3' miRNA:   3'- -GCUGac--UGCUGCUGGGGa-----C-GGGCaua -5'
12591	5'	-58	NC_003345.1	+	48984	0.66	0.643803
	Target:  5'- cCGACUcuaccgcuucugGAgGuagcauccGCGACCCCUGCuuGUGUu -3' miRNA:   3'- -GCUGA------------CUgC--------UGCUGGGGACGggCAUA- -5'
12591	5'	-58	NC_003345.1	+	48753	0.72	0.354237
	Target:  5'- uGACUGACG-CGACCUCccgGCCCa--- -3' miRNA:   3'- gCUGACUGCuGCUGGGGa--CGGGcaua -5'
12591	5'	-58	NC_003345.1	+	68731	0.74	0.247721
	Target:  5'- gGACaUGAgGGCGACCuUCUGCCCGUu- -3' miRNA:   3'- gCUG-ACUgCUGCUGG-GGACGGGCAua -5'
12591	5'	-58	NC_003345.1	+	7831	1.05	0.001692
	Target:  5'- gCGACUGACGACGACCCCUGCCCGUAUc -3' miRNA:   3'- -GCUGACUGCUGCUGGGGACGGGCAUA- -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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