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
30961	3'	-54.4	NC_006556.1	+	8982	0.66	0.530158
	Target:  5'- cCCAGaaauccCCACCACCgGUaAUggGAAUCCa -3' miRNA:   3'- -GGUU------GGUGGUGGgCGgUGagCUUAGG- -5'
30961	3'	-54.4	NC_006556.1	+	11782	0.66	0.496681
	Target:  5'- cCCAACUACCGCCCcaacaacuaaaGCCAacgcCGAAa-- -3' miRNA:   3'- -GGUUGGUGGUGGG-----------CGGUga--GCUUagg -5'
30961	3'	-54.4	NC_006556.1	+	7486	0.66	0.495581
	Target:  5'- cCCAACCGCgucaguaUACCgGCUAUguaaaGggUCCu -3' miRNA:   3'- -GGUUGGUG-------GUGGgCGGUGag---CuuAGG- -5'
30961	3'	-54.4	NC_006556.1	+	7781	0.67	0.453606
	Target:  5'- aCGugUcCCACCCGCCACagcCGAAa-- -3' miRNA:   3'- gGUugGuGGUGGGCGGUGa--GCUUagg -5'
30961	3'	-54.4	NC_006556.1	+	12446	0.68	0.393034
	Target:  5'- gCAACCACCAuaUCgGCCAUga-AGUCCa -3' miRNA:   3'- gGUUGGUGGU--GGgCGGUGagcUUAGG- -5'
30961	3'	-54.4	NC_006556.1	+	1355	0.72	0.207438
	Target:  5'- aCAGCCACggauCACCCGCCaaguccaacauGCUUGAGcCCu -3' miRNA:   3'- gGUUGGUG----GUGGGCGG-----------UGAGCUUaGG- -5'
30961	3'	-54.4	NC_006556.1	+	13781	1.14	0.000169
	Target:  5'- aCCAACCACCACCCGCCACUCGAAUCCu -3' miRNA:   3'- -GGUUGGUGGUGGGCGGUGAGCUUAGG- -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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