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
14715	3'	-53.2	NC_003529.1	+	31104	0.66	0.97613
	Target:  5'- cCAuCGUUgUCGAcg--GCCCGGGGCAa -3' miRNA:   3'- cGUuGCGA-AGCUuugaCGGGCCCUGU- -5'
14715	3'	-53.2	NC_003529.1	+	144411	0.66	0.973511
	Target:  5'- aGCAAUGUaUUCGAGACcgucgcgGCCCGuGACc -3' miRNA:   3'- -CGUUGCG-AAGCUUUGa------CGGGCcCUGu -5'
14715	3'	-53.2	NC_003529.1	+	76499	0.66	0.967658
	Target:  5'- --uGCGCUUgGuacGACUGCcacgaggccugCCGGGACGa -3' miRNA:   3'- cguUGCGAAgCu--UUGACG-----------GGCCCUGU- -5'
14715	3'	-53.2	NC_003529.1	+	22672	0.66	0.964412
	Target:  5'- cGUAugGCU--GAuAUUGCCCaGGACGu -3' miRNA:   3'- -CGUugCGAagCUuUGACGGGcCCUGU- -5'
14715	3'	-53.2	NC_003529.1	+	57933	0.67	0.960943
	Target:  5'- -aAGCGCUUCGAua--GCuuGGGugAu -3' miRNA:   3'- cgUUGCGAAGCUuugaCGggCCCugU- -5'
14715	3'	-53.2	NC_003529.1	+	116528	0.68	0.930086
	Target:  5'- uGCAACGCUaCGAAAacaacaaauaUGCCgaguguggCGGGACu -3' miRNA:   3'- -CGUUGCGAaGCUUUg---------ACGG--------GCCCUGu -5'
14715	3'	-53.2	NC_003529.1	+	21112	1.1	0.004456
	Target:  5'- uGCAACGCUUCGAAACUGCCCGGGACAc -3' miRNA:   3'- -CGUUGCGAAGCUUUGACGGGCCCUGU- -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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