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
18540	5'	-59.1	NC_004682.1	+	50265	1.09	0.00046
	Target:  5'- uCUCCGUAUGGCGGGCCAGUCGUCGGGu -3' miRNA:   3'- -GAGGCAUACCGCCCGGUCAGCAGCCC- -5'
18540	5'	-59.1	NC_004682.1	+	3166	0.7	0.308168
	Target:  5'- aCUCgGgcaccacGGCGGGCCAGggCG-CGGGc -3' miRNA:   3'- -GAGgCaua----CCGCCCGGUCa-GCaGCCC- -5'
18540	5'	-59.1	NC_004682.1	+	45560	0.67	0.452596
	Target:  5'- -aCCGU-UGGCGuacuccucgguGGCCcggaAGUCGUCGGa -3' miRNA:   3'- gaGGCAuACCGC-----------CCGG----UCAGCAGCCc -5'
18540	5'	-59.1	NC_004682.1	+	22977	0.67	0.452596
	Target:  5'- cCUCCGggcUGGCcuucGGGCUGGUC--CGGGg -3' miRNA:   3'- -GAGGCau-ACCG----CCCGGUCAGcaGCCC- -5'
18540	5'	-59.1	NC_004682.1	+	37545	0.67	0.462196
	Target:  5'- gCUCCac----CGGGCCGG-CGUCGGGu -3' miRNA:   3'- -GAGGcauaccGCCCGGUCaGCAGCCC- -5'
18540	5'	-59.1	NC_004682.1	+	42636	0.67	0.485662
	Target:  5'- -cCCGgcacgccacaagGGCGGuCCAGUCGUUGGa -3' miRNA:   3'- gaGGCaua---------CCGCCcGGUCAGCAGCCc -5'
18540	5'	-59.1	NC_004682.1	+	23680	0.66	0.521875
	Target:  5'- -gCCGa---GCaGGGCCacacGGUCGUCGGGu -3' miRNA:   3'- gaGGCauacCG-CCCGG----UCAGCAGCCC- -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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