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
13282	3'	-58	NC_003409.1	+	53295	0.66	0.786114
	Target:  5'- uGGUcaGGUcgccgcGGCGCACCACCUGg-GAGg -3' miRNA:   3'- gCCA--UCAa-----CCGCGUGGUGGGCgaCUU- -5'
13282	3'	-58	NC_003409.1	+	60485	0.66	0.776824
	Target:  5'- uGGgAGUUGGCGCugCGaCUGCaGAAu -3' miRNA:   3'- gCCaUCAACCGCGugGUgGGCGaCUU- -5'
13282	3'	-58	NC_003409.1	+	30975	0.66	0.776824
	Target:  5'- gGGUGGguucagcgggUGGUGCGCCAacuaCCGC-GAGu -3' miRNA:   3'- gCCAUCa---------ACCGCGUGGUg---GGCGaCUU- -5'
13282	3'	-58	NC_003409.1	+	126392	0.67	0.738451
	Target:  5'- aGGcGGUUGGCGUggcggaguAUCGCCauCGCUGGAu -3' miRNA:   3'- gCCaUCAACCGCG--------UGGUGG--GCGACUU- -5'
13282	3'	-58	NC_003409.1	+	49278	0.67	0.7286
	Target:  5'- aCGGUGGcccugccuaguggggUGGCGCGCCACagucgagCCGCcagGAAc -3' miRNA:   3'- -GCCAUCa--------------ACCGCGUGGUG-------GGCGa--CUU- -5'
13282	3'	-58	NC_003409.1	+	33987	0.67	0.718666
	Target:  5'- gGGUAcg-GGCGCGCCagggacagcGCCCGCcaUGGAc -3' miRNA:   3'- gCCAUcaaCCGCGUGG---------UGGGCG--ACUU- -5'
13282	3'	-58	NC_003409.1	+	31145	1.06	0.002485
	Target:  5'- gCGGUAGUUGGCGCACCACCCGCUGAAc -3' miRNA:   3'- -GCCAUCAACCGCGUGGUGGGCGACUU- -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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