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
22441	3'	-56.2	NC_005056.1	+	25909	0.66	0.482012
	Target:  5'- -cGCGUG-GCUGAcggauaagcugcacgACGGgcagCAGGUAUUg -3' miRNA:   3'- gaCGCGCuCGACU---------------UGCCa---GUCCGUAG- -5'
22441	3'	-56.2	NC_005056.1	+	12558	0.67	0.45067
	Target:  5'- -cGCGCuacuGAGCUGGacaaggccuuuucgcGCGGUgGuGGCGUCc -3' miRNA:   3'- gaCGCG----CUCGACU---------------UGCCAgU-CCGUAG- -5'
22441	3'	-56.2	NC_005056.1	+	17070	0.67	0.446576
	Target:  5'- uUGCGCG-GCauUGccauCGGUCAGGC-UCc -3' miRNA:   3'- gACGCGCuCG--ACuu--GCCAGUCCGuAG- -5'
22441	3'	-56.2	NC_005056.1	+	16570	0.67	0.436432
	Target:  5'- -gGCacCGAuGCUGAccugcuuaACGaGUCAGGCGUCa -3' miRNA:   3'- gaCGc-GCU-CGACU--------UGC-CAGUCCGUAG- -5'
22441	3'	-56.2	NC_005056.1	+	16364	0.7	0.294043
	Target:  5'- -aGCGUGAGCUGA-UGGUCAucuGGCc-- -3' miRNA:   3'- gaCGCGCUCGACUuGCCAGU---CCGuag -5'
22441	3'	-56.2	NC_005056.1	+	6708	0.71	0.237632
	Target:  5'- -gGCGCGGuCUGAAC-GUCGGGCAguUCg -3' miRNA:   3'- gaCGCGCUcGACUUGcCAGUCCGU--AG- -5'
22441	3'	-56.2	NC_005056.1	+	18138	1.09	0.000354
	Target:  5'- aCUGCGCGAGCUGAACGGUCAGGCAUCc -3' miRNA:   3'- -GACGCGCUCGACUUGCCAGUCCGUAG- -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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