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
23671	5'	-57.9	NC_005261.1	+	92779	0.66	0.846291
	Target:  5'- -cCGAgcccGGGCUCggGGUCGGGGUcCGGu -3' miRNA:   3'- cuGCU----CCUGAGgaCCAGCCUCA-GCCu -5'
23671	5'	-57.9	NC_005261.1	+	128881	0.66	0.813309
	Target:  5'- cGACGAGG-CgggggCCgGGUgGGAGgCGGGc -3' miRNA:   3'- -CUGCUCCuGa----GGaCCAgCCUCaGCCU- -5'
23671	5'	-57.9	NC_005261.1	+	64518	0.68	0.720871
	Target:  5'- cGCGGGcGGCUCCUcGUCGGGGggcaggucCGGGa -3' miRNA:   3'- cUGCUC-CUGAGGAcCAGCCUCa-------GCCU- -5'
23671	5'	-57.9	NC_005261.1	+	65792	0.68	0.701217
	Target:  5'- cGGCG-GGAacaUCCgcgGGUCGGGGUgccCGGGc -3' miRNA:   3'- -CUGCuCCUg--AGGa--CCAGCCUCA---GCCU- -5'
23671	5'	-57.9	NC_005261.1	+	98669	0.69	0.681337
	Target:  5'- aGGCGAGGgcggGCUCCgccggGGcCGGAGgcgCGGc -3' miRNA:   3'- -CUGCUCC----UGAGGa----CCaGCCUCa--GCCu -5'
23671	5'	-57.9	NC_005261.1	+	34881	0.72	0.5218
	Target:  5'- cGACGAcacGGAgUCg-GaGUCGGAGUCGGAc -3' miRNA:   3'- -CUGCU---CCUgAGgaC-CAGCCUCAGCCU- -5'
23671	5'	-57.9	NC_005261.1	+	34812	1.08	0.002152
	Target:  5'- gGACGAGGACUCCUGGUCGGAGUCGGAg -3' miRNA:   3'- -CUGCUCCUGAGGACCAGCCUCAGCCU- -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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