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
2338	3'	-54.4	NC_001416.1	+	43713	0.7	0.442063
	Target:  5'- gCGCGGACacguUCAUCuuuGGUCAuacGCCAGCAg -3' miRNA:   3'- -GUGCUUG----AGUAGuc-CCAGU---CGGUCGU- -5'
2338	3'	-54.4	NC_001416.1	+	16152	0.69	0.536624
	Target:  5'- -gUGGACUCGgagCAGuucGG-CAGCCAGCAg -3' miRNA:   3'- guGCUUGAGUa--GUC---CCaGUCGGUCGU- -5'
2338	3'	-54.4	NC_001416.1	+	19531	0.67	0.62595
	Target:  5'- gACGGAUUCAUCguuGGGGUCGGUUAuaAa -3' miRNA:   3'- gUGCUUGAGUAG---UCCCAGUCGGUcgU- -5'
2338	3'	-54.4	NC_001416.1	+	21721	0.67	0.637244
	Target:  5'- aACGGACa-GUCAGGG-CAGCCA-CAg -3' miRNA:   3'- gUGCUUGagUAGUCCCaGUCGGUcGU- -5'
2338	3'	-54.4	NC_001416.1	+	13998	0.66	0.693416
	Target:  5'- cCGCGAuagguC-CAggugCAGGuGUUGGCCAGCAu -3' miRNA:   3'- -GUGCUu----GaGUa---GUCC-CAGUCGGUCGU- -5'
2338	3'	-54.4	NC_001416.1	+	5636	0.66	0.686728
	Target:  5'- gGCGGGC-CGUUuucacggucauaccgGGGGUUucuGCCAGCAc -3' miRNA:   3'- gUGCUUGaGUAG---------------UCCCAGu--CGGUCGU- -5'
2338	3'	-54.4	NC_001416.1	+	7184	1.09	0.000896
	Target:  5'- aCACGAACUCAUCAGGGUCAGCCAGCAg -3' miRNA:   3'- -GUGCUUGAGUAGUCCCAGUCGGUCGU- -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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