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
22950	3'	-58.7	NC_005137.2	+	44102	0.66	0.764847
	Target:  5'- uAUCGCUGCUGGUGcUGGacGCGuGggUg -3' miRNA:   3'- uUAGCGACGGCCACaGCC--CGC-CuuGu -5'
22950	3'	-58.7	NC_005137.2	+	73949	0.66	0.764847
	Target:  5'- aGAUCGCUGCCGGUcagaauuaaCGcGGUGGucacguACAa -3' miRNA:   3'- -UUAGCGACGGCCAca-------GC-CCGCCu-----UGU- -5'
22950	3'	-58.7	NC_005137.2	+	23042	0.66	0.726117
	Target:  5'- -cUCGCUGgaGGUGUucacCGuGGCGGAcgACAa -3' miRNA:   3'- uuAGCGACggCCACA----GC-CCGCCU--UGU- -5'
22950	3'	-58.7	NC_005137.2	+	19806	0.66	0.726117
	Target:  5'- --aUGCUGCUGGUagCGGGCGcAACGc -3' miRNA:   3'- uuaGCGACGGCCAcaGCCCGCcUUGU- -5'
22950	3'	-58.7	NC_005137.2	+	124986	0.67	0.706228
	Target:  5'- --gCGCUGCguUGGaaaUCGGGCGGGAUg -3' miRNA:   3'- uuaGCGACG--GCCac-AGCCCGCCUUGu -5'
22950	3'	-58.7	NC_005137.2	+	108124	0.69	0.553791
	Target:  5'- cGAUCGCaGCaccgcauccCGGUcGUCGGGCGGcGGCGg -3' miRNA:   3'- -UUAGCGaCG---------GCCA-CAGCCCGCC-UUGU- -5'
22950	3'	-58.7	NC_005137.2	+	71079	0.76	0.227306
	Target:  5'- aAAUUGCUGCaaaucaaUGUCGGGCGGAGCGu -3' miRNA:   3'- -UUAGCGACGgcc----ACAGCCCGCCUUGU- -5'
22950	3'	-58.7	NC_005137.2	+	81681	1.06	0.002091
	Target:  5'- gAAUCGCUGCCGGUGUCGGGCGGAACAc -3' miRNA:   3'- -UUAGCGACGGCCACAGCCCGCCUUGU- -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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