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
28263	5'	-51	NC_005902.1	+	112674	0.67	0.99179
	Target:  5'- ----aUCCUGG-UCAUCAaGGAauaagaGGACCu -3' miRNA:   3'- aaauaAGGACCuAGUGGU-CCU------CCUGG- -5'
28263	5'	-51	NC_005902.1	+	72701	0.68	0.979673
	Target:  5'- ----cUCCagGGAgaccauuuuuaccaUCuauACCAGGAGGACCc -3' miRNA:   3'- aaauaAGGa-CCU--------------AG---UGGUCCUCCUGG- -5'
28263	5'	-51	NC_005902.1	+	73278	0.7	0.933276
	Target:  5'- ---cUUCCaGGGUCACCAGGcauuccAGGAgCu -3' miRNA:   3'- aaauAAGGaCCUAGUGGUCC------UCCUgG- -5'
28263	5'	-51	NC_005902.1	+	72890	0.74	0.782614
	Target:  5'- -----aCCaGGAaUACCAGGAGGACCn -3' miRNA:   3'- aaauaaGGaCCUaGUGGUCCUCCUGG- -5'
28263	5'	-51	NC_005902.1	+	73371	0.77	0.671567
	Target:  5'- cUUAUUCCUugaugaccaGGAUUACCAGGcucacccauAGGGCCu -3' miRNA:   3'- aAAUAAGGA---------CCUAGUGGUCC---------UCCUGG- -5'
28263	5'	-51	NC_005902.1	+	72666	0.78	0.618931
	Target:  5'- -----aCCaGGAggACCAGGAGGACCa -3' miRNA:   3'- aaauaaGGaCCUagUGGUCCUCCUGG- -5'
28263	5'	-51	NC_005902.1	+	72911	1.1	0.008017
	Target:  5'- aUUUAUUCCUGGAUCACCAGGAGGACCu -3' miRNA:   3'- -AAAUAAGGACCUAGUGGUCCUCCUGG- -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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