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
31904	3'	-56.5	NC_006938.1	+	52950	0.66	0.704318
	Target:  5'- --aCGUCGaGG-CUCCCGaggguggugcauCGACCAGCu -3' miRNA:   3'- cgaGCAGC-CCaGAGGGU------------GCUGGUUGc -5'
31904	3'	-56.5	NC_006938.1	+	22760	0.67	0.692826
	Target:  5'- uCUUGgcaCGGGcCUCCUugGACCGcuggaggACGg -3' miRNA:   3'- cGAGCa--GCCCaGAGGGugCUGGU-------UGC- -5'
31904	3'	-56.5	NC_006938.1	+	12888	0.7	0.474423
	Target:  5'- cGCUCGcCGGGgccUCUCCCGCcuccuugGGCuCGACa -3' miRNA:   3'- -CGAGCaGCCC---AGAGGGUG-------CUG-GUUGc -5'
31904	3'	-56.5	NC_006938.1	+	9603	0.73	0.357922
	Target:  5'- -gUCGUCGGGgcugaCUCCCGCugGACCuuCGa -3' miRNA:   3'- cgAGCAGCCCa----GAGGGUG--CUGGuuGC- -5'
31904	3'	-56.5	NC_006938.1	+	52642	0.75	0.262336
	Target:  5'- uCUCGUCGGGUUUCgaGCGGCgCAACa -3' miRNA:   3'- cGAGCAGCCCAGAGggUGCUG-GUUGc -5'
31904	3'	-56.5	NC_006938.1	+	37479	0.77	0.198599
	Target:  5'- uGCUUGcCGGGgacucCUCCgCGCGACCAGCu -3' miRNA:   3'- -CGAGCaGCCCa----GAGG-GUGCUGGUUGc -5'
31904	3'	-56.5	NC_006938.1	+	58195	1.1	0.000912
	Target:  5'- cGCUCGUCGGGUCUCCCACGACCAACGu -3' miRNA:   3'- -CGAGCAGCCCAGAGGGUGCUGGUUGC- -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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