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
12723	3'	-53.2	NC_003356.1	+	23588	0.66	0.721001
	Target:  5'- -uGCGAcugucugucacaUCAGcgCUGUAGAUugUGUCg -3' miRNA:   3'- ucCGCU------------AGUCaaGACGUCUGugACGG- -5'
12723	3'	-53.2	NC_003356.1	+	27850	0.69	0.57323
	Target:  5'- aAGGUGGcUCAGc----CAGGCGCUGCCg -3' miRNA:   3'- -UCCGCU-AGUCaagacGUCUGUGACGG- -5'
12723	3'	-53.2	NC_003356.1	+	120	0.7	0.51747
	Target:  5'- -uGCGAUCuGUUCUGCAu-UGCUGUCa -3' miRNA:   3'- ucCGCUAGuCAAGACGUcuGUGACGG- -5'
12723	3'	-53.2	NC_003356.1	+	29191	0.76	0.235833
	Target:  5'- aGGGCGGUCAGUUCcu--GACcCUGCCc -3' miRNA:   3'- -UCCGCUAGUCAAGacguCUGuGACGG- -5'
12723	3'	-53.2	NC_003356.1	+	20889	1.13	0.000547
	Target:  5'- cAGGCGAUCAGUUCUGCAGACACUGCCg -3' miRNA:   3'- -UCCGCUAGUCAAGACGUCUGUGACGG- -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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