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
17305	5'	-46.4	NC_004367.1	+	10877	0.66	0.999873
	Target:  5'- -cUCUGUGGCCAUAcgcaCCGAUGAc-- -3' miRNA:   3'- ccAGAUACCGGUAUuc--GGUUAUUcuu -5'
17305	5'	-46.4	NC_004367.1	+	7778	0.66	0.999806
	Target:  5'- -cUCUcUGGCCAgcgagcaucuagcGGCCGGUGAGAc -3' miRNA:   3'- ccAGAuACCGGUau-----------UCGGUUAUUCUu -5'
17305	5'	-46.4	NC_004367.1	+	27879	0.68	0.998669
	Target:  5'- cGUCUuucGUGGCC-UGGGCC--UAAGGAa -3' miRNA:   3'- cCAGA---UACCGGuAUUCGGuuAUUCUU- -5'
17305	5'	-46.4	NC_004367.1	+	52012	0.72	0.980064
	Target:  5'- aGUCUGUGGCCAUAgacuuaagaucguaAGUaggaAAUAAGAc -3' miRNA:   3'- cCAGAUACCGGUAU--------------UCGg---UUAUUCUu -5'
17305	5'	-46.4	NC_004367.1	+	79722	0.73	0.969772
	Target:  5'- cGUCUAuaguaaUGGCCAUAAGCCccccaccUAGGAGc -3' miRNA:   3'- cCAGAU------ACCGGUAUUCGGuu-----AUUCUU- -5'
17305	5'	-46.4	NC_004367.1	+	128756	0.94	0.158804
	Target:  5'- gGGUCUAUGGCCAUAAGC-AAUAAGAAc -3' miRNA:   3'- -CCAGAUACCGGUAUUCGgUUAUUCUU- -5'
17305	5'	-46.4	NC_004367.1	+	122938	1.09	0.019809
	Target:  5'- gGGUCUAUGGCCAUAAGCCAAUAAGAAc -3' miRNA:   3'- -CCAGAUACCGGUAUUCGGUUAUUCUU- -5'
17305	5'	-46.4	NC_004367.1	+	125847	1.09	0.019809
	Target:  5'- gGGUCUAUGGCCAUAAGCCAAUAAGAAc -3' miRNA:   3'- -CCAGAUACCGGUAUUCGGUUAUUCUU- -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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