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
11396	3'	-46.7	NC_003084.1	+	102870	0.66	0.99954
	Target:  5'- uGCUGUCGGUgcucACAuuggUCGGAAUa -3' miRNA:   3'- gCGACAGCCAau--UGUcga-AGCUUUAc -5'
11396	3'	-46.7	NC_003084.1	+	9469	0.66	0.999408
	Target:  5'- aGCUGggcgcacCGGUcuACAGCUUUGAugguuguAGUGg -3' miRNA:   3'- gCGACa------GCCAauUGUCGAAGCU-------UUAC- -5'
11396	3'	-46.7	NC_003084.1	+	73489	0.66	0.999276
	Target:  5'- uCGC-GUUGGUgaaguACAGCaggUCGAAGUa -3' miRNA:   3'- -GCGaCAGCCAau---UGUCGa--AGCUUUAc -5'
11396	3'	-46.7	NC_003084.1	+	29135	0.67	0.998891
	Target:  5'- aGCUGagcguaUCGGUcaccucACAGC-UCGAAAUGu -3' miRNA:   3'- gCGAC------AGCCAau----UGUCGaAGCUUUAC- -5'
11396	3'	-46.7	NC_003084.1	+	56716	0.71	0.978042
	Target:  5'- aCGCuaugUGUCGGUUGcCAuCUUCGAGAUa -3' miRNA:   3'- -GCG----ACAGCCAAUuGUcGAAGCUUUAc -5'
11396	3'	-46.7	NC_003084.1	+	65513	0.71	0.977786
	Target:  5'- aCGCUcgggugaGUCGGUUcGCGGCU-CGAAAg- -3' miRNA:   3'- -GCGA-------CAGCCAAuUGUCGAaGCUUUac -5'
11396	3'	-46.7	NC_003084.1	+	85923	1.09	0.015906
	Target:  5'- cCGCUGUCGGUUAACAGCUUCGAAAUGc -3' miRNA:   3'- -GCGACAGCCAAUUGUCGAAGCUUUAC- -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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