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
27990	3'	-56.2	NC_005886.2	+	26920	0.67	0.603217
	Target:  5'- gGUUGcCGGuCgCguagUGCCGcCCGGGCg -3' miRNA:   3'- gCAGCuGUCuG-Gaa--ACGGCaGGCCCG- -5'
27990	3'	-56.2	NC_005886.2	+	15103	0.67	0.581493
	Target:  5'- aCG-CGACguAGGCUguuggcgUGCCGUCCGGa- -3' miRNA:   3'- -GCaGCUG--UCUGGaa-----ACGGCAGGCCcg -5'
27990	3'	-56.2	NC_005886.2	+	41394	0.68	0.537542
	Target:  5'- --aCGGCAGACCUuccguauccagaUcgagcgugcgaacUGCCGUUuCGGGCg -3' miRNA:   3'- gcaGCUGUCUGGA------------A-------------ACGGCAG-GCCCG- -5'
27990	3'	-56.2	NC_005886.2	+	39807	0.69	0.476515
	Target:  5'- cCGUCGAauuucCAGACUcgUUGCUuaUCGGGCg -3' miRNA:   3'- -GCAGCU-----GUCUGGa-AACGGcaGGCCCG- -5'
27990	3'	-56.2	NC_005886.2	+	29515	0.7	0.408892
	Target:  5'- gCGUUGACGGGugUU--CCGUCCGGGUu -3' miRNA:   3'- -GCAGCUGUCUggAAacGGCAGGCCCG- -5'
27990	3'	-56.2	NC_005886.2	+	29704	0.72	0.331315
	Target:  5'- aCGUCgGGCGuACCUUcGCCGUCgcacuuCGGGCa -3' miRNA:   3'- -GCAG-CUGUcUGGAAaCGGCAG------GCCCG- -5'
27990	3'	-56.2	NC_005886.2	+	40494	1.13	0.000422
	Target:  5'- aCGUCGACAGACCUUUGCCGUCCGGGCg -3' miRNA:   3'- -GCAGCUGUCUGGAAACGGCAGGCCCG- -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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