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
11876	3'	-57.3	NC_003266.2	+	5408	0.65	0.530213
	Target:  5'- cCUCCUCUgucccgCCUGugggcagacuuccaAAGGUaagCUCCGCGc -3' miRNA:   3'- aGAGGAGGa-----GGAC--------------UUCCA---GAGGCGCc -5'
11876	3'	-57.3	NC_003266.2	+	17803	0.67	0.440709
	Target:  5'- gCUCCUCCUCCaccugcGGcaUCUCCaCGGa -3' miRNA:   3'- aGAGGAGGAGGacuu--CC--AGAGGcGCC- -5'
11876	3'	-57.3	NC_003266.2	+	23734	0.68	0.402519
	Target:  5'- gCUCCUCCaCgCUGAGGGgcacCUCggUGCGGu -3' miRNA:   3'- aGAGGAGGaG-GACUUCCa---GAG--GCGCC- -5'
11876	3'	-57.3	NC_003266.2	+	2146	0.69	0.316762
	Target:  5'- aCUCCUCCgCCgGAGGGUCcaggCCGgcucuCGGa -3' miRNA:   3'- aGAGGAGGaGGaCUUCCAGa---GGC-----GCC- -5'
11876	3'	-57.3	NC_003266.2	+	27155	0.71	0.251994
	Target:  5'- aCUCCgugggCCgggcCCUGAGGGUgCUCCuCGGa -3' miRNA:   3'- aGAGGa----GGa---GGACUUCCA-GAGGcGCC- -5'
11876	3'	-57.3	NC_003266.2	+	23545	0.71	0.245513
	Target:  5'- gCUCCUCCUCgUG-----CUCCGCGGg -3' miRNA:   3'- aGAGGAGGAGgACuuccaGAGGCGCC- -5'
11876	3'	-57.3	NC_003266.2	+	8712	1.1	0.000348
	Target:  5'- aUCUCCUCCUCCUGAAGGUCUCCGCGGc -3' miRNA:   3'- -AGAGGAGGAGGACUUCCAGAGGCGCC- -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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