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
1403	3'	-58.1	NC_001335.1	+	26673	0.67	0.504214
	Target:  5'- aCGgCCGGCUCaaggCCGUUCGGcucgGUCCc -3' miRNA:   3'- -GUgGGUCGAGag--GGCAAGCCa---CAGGu -5'
1403	3'	-58.1	NC_001335.1	+	28178	0.67	0.483885
	Target:  5'- gACCCAucaGCUCUUcaucgagaCCGUUCGGUG-CUg -3' miRNA:   3'- gUGGGU---CGAGAG--------GGCAAGCCACaGGu -5'
1403	3'	-58.1	NC_001335.1	+	22030	0.68	0.444466
	Target:  5'- aGCCCGGauggCCUGUUCGGUguaGUCCu -3' miRNA:   3'- gUGGGUCgagaGGGCAAGCCA---CAGGu -5'
1403	3'	-58.1	NC_001335.1	+	36818	0.68	0.406001
	Target:  5'- uGCgCCAGgUCUacgacggCCCGgUUGGUGUCCAc -3' miRNA:   3'- gUG-GGUCgAGA-------GGGCaAGCCACAGGU- -5'
1403	3'	-58.1	NC_001335.1	+	22521	0.7	0.338087
	Target:  5'- gCGCCCGGUgagggCUCCCcagaacuuGUUCcaGGUGUCCu -3' miRNA:   3'- -GUGGGUCGa----GAGGG--------CAAG--CCACAGGu -5'
1403	3'	-58.1	NC_001335.1	+	17902	0.75	0.165303
	Target:  5'- aGCCCAGCgagaaUCCCGgaggggUCGGUGcCCGa -3' miRNA:   3'- gUGGGUCGag---AGGGCa-----AGCCACaGGU- -5'
1403	3'	-58.1	NC_001335.1	+	41386	1.07	0.000646
	Target:  5'- uCACCCAGCUCUCCCGUUCGGUGUCCAu -3' miRNA:   3'- -GUGGGUCGAGAGGGCAAGCCACAGGU- -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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