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
17982	5'	-52.9	NC_004665.1	+	12552	0.66	0.731918
	Target:  5'- -uUGAUCCCGUUGuGGaaCACGAugagaccauccGGCu -3' miRNA:   3'- ucACUAGGGCAACcCCaaGUGUU-----------CCG- -5'
17982	5'	-52.9	NC_004665.1	+	18885	0.67	0.675664
	Target:  5'- -aUGGaCaCCGcUGGGGUUCAacCGGGGCc -3' miRNA:   3'- ucACUaG-GGCaACCCCAAGU--GUUCCG- -5'
17982	5'	-52.9	NC_004665.1	+	24888	0.67	0.652758
	Target:  5'- cGGaUGGUCCC-UUGGu-UUCGCAGGGCc -3' miRNA:   3'- -UC-ACUAGGGcAACCccAAGUGUUCCG- -5'
17982	5'	-52.9	NC_004665.1	+	23057	0.68	0.62977
	Target:  5'- gAGUGAUggugCCCGUcccuaUGGGauuggUCGCGGGGUu -3' miRNA:   3'- -UCACUA----GGGCA-----ACCCca---AGUGUUCCG- -5'
17982	5'	-52.9	NC_004665.1	+	27224	0.71	0.462972
	Target:  5'- cGGUGucggCCCaUUGaGGGUUCucaGCGAGGCc -3' miRNA:   3'- -UCACua--GGGcAAC-CCCAAG---UGUUCCG- -5'
17982	5'	-52.9	NC_004665.1	+	22570	0.73	0.329744
	Target:  5'- cAGUGAUcuccacgagguaaCCCGgugGGGcGUUCGCAGGGa -3' miRNA:   3'- -UCACUA-------------GGGCaa-CCC-CAAGUGUUCCg -5'
17982	5'	-52.9	NC_004665.1	+	18262	1.11	0.000726
	Target:  5'- gAGUGAUCCCGUUGGGGUUCACAAGGCc -3' miRNA:   3'- -UCACUAGGGCAACCCCAAGUGUUCCG- -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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