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
30939	5'	-56.2	NC_006552.1	+	33050	0.66	0.684565
	Target:  5'- cUUCUgCGACUCGGGCaac--UCGGCGUa -3' miRNA:   3'- -AAGA-GCUGGGCUCGcaacuAGCCGCG- -5'
30939	5'	-56.2	NC_006552.1	+	28286	0.68	0.609088
	Target:  5'- -cCUCGGCCCGAucGCGUUGAagUGGauCg -3' miRNA:   3'- aaGAGCUGGGCU--CGCAACUa-GCCgcG- -5'
30939	5'	-56.2	NC_006552.1	+	34233	0.68	0.609088
	Target:  5'- -gCUCGACUCG-GCuuccgaGUUGuacgCGGCGCa -3' miRNA:   3'- aaGAGCUGGGCuCG------CAACua--GCCGCG- -5'
30939	5'	-56.2	NC_006552.1	+	14746	0.68	0.587557
	Target:  5'- -gCUCGGCCuUGAucuGCGgcauGUCGGCGCg -3' miRNA:   3'- aaGAGCUGG-GCU---CGCaac-UAGCCGCG- -5'
30939	5'	-56.2	NC_006552.1	+	18306	0.68	0.566171
	Target:  5'- -cCUCG-CCCGGGCGcagcacugGAacUUGGCGCc -3' miRNA:   3'- aaGAGCuGGGCUCGCaa------CU--AGCCGCG- -5'
30939	5'	-56.2	NC_006552.1	+	20982	0.7	0.483222
	Target:  5'- -gCUCGGCgcguCCGGGaUGUUGAucggaaucauugUCGGCGCg -3' miRNA:   3'- aaGAGCUG----GGCUC-GCAACU------------AGCCGCG- -5'
30939	5'	-56.2	NC_006552.1	+	45385	0.72	0.371214
	Target:  5'- ---gCGGCCCGGGCucUUGcUCGGCGCc -3' miRNA:   3'- aagaGCUGGGCUCGc-AACuAGCCGCG- -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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