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
4384	3'	-59.7	NC_001720.1	+	17407	0.66	0.413699
	Target:  5'- aCACCUCCg--GGC-CCgCCUCUGUAa- -3' miRNA:   3'- -GUGGGGGauaCCGuGG-GGGGACAUgu -5'
4384	3'	-59.7	NC_001720.1	+	34716	0.66	0.404441
	Target:  5'- uCGCCCCUaGUGacgucagaguGcCACgCCCCUUGUACAg -3' miRNA:   3'- -GUGGGGGaUAC----------C-GUG-GGGGGACAUGU- -5'
4384	3'	-59.7	NC_001720.1	+	39917	0.67	0.340151
	Target:  5'- cCACCCCCUAccuguaccgauaaGGCACa-CCCUGaGCAa -3' miRNA:   3'- -GUGGGGGAUa------------CCGUGggGGGACaUGU- -5'
4384	3'	-59.7	NC_001720.1	+	28160	0.69	0.242156
	Target:  5'- uCACCCCCgcgucuggGUcGGUACCCCCCggaucGCGc -3' miRNA:   3'- -GUGGGGGa-------UA-CCGUGGGGGGaca--UGU- -5'
4384	3'	-59.7	NC_001720.1	+	37266	0.83	0.02527
	Target:  5'- -cCCCCCUGUa-CACCCCCCUGUACAa -3' miRNA:   3'- guGGGGGAUAccGUGGGGGGACAUGU- -5'
4384	3'	-59.7	NC_001720.1	+	37316	0.94	0.003686
	Target:  5'- cCACCCCCcAUGGaCACCCCCCUGUACAu -3' miRNA:   3'- -GUGGGGGaUACC-GUGGGGGGACAUGU- -5'
4384	3'	-59.7	NC_001720.1	+	37239	1.07	0.000321
	Target:  5'- cCACCCCCUAUGGCACCCCCCUGUACAc -3' miRNA:   3'- -GUGGGGGAUACCGUGGGGGGACAUGU- -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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