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
8906	5'	-54.2	NC_002484.1	+	43138	0.83	0.102627
	Target:  5'- cCGUGGCCGACCGCcguccauGCGACGCCc -3' miRNA:   3'- -GCAUCGGCUGGCGaacu---UGCUGUGGc -5'
8906	5'	-54.2	NC_002484.1	+	54101	0.7	0.58004
	Target:  5'- --cAGCCGACCGCUauaccucUGAGCuACACg- -3' miRNA:   3'- gcaUCGGCUGGCGA-------ACUUGcUGUGgc -5'
8906	5'	-54.2	NC_002484.1	+	9423	0.67	0.732902
	Target:  5'- aGUcGcCCGugCGUUUGAACaGACgACCGu -3' miRNA:   3'- gCAuC-GGCugGCGAACUUG-CUG-UGGC- -5'
8906	5'	-54.2	NC_002484.1	+	19318	0.67	0.763893
	Target:  5'- aCGUAG-UGGCCGCcUGGcgcaugcacauGCGGCGCCc -3' miRNA:   3'- -GCAUCgGCUGGCGaACU-----------UGCUGUGGc -5'
8906	5'	-54.2	NC_002484.1	+	54703	0.66	0.77397
	Target:  5'- uGUuGCCaGCCGCaUGcaGAUGGCGCCGc -3' miRNA:   3'- gCAuCGGcUGGCGaAC--UUGCUGUGGC- -5'
8906	5'	-54.2	NC_002484.1	+	4935	0.66	0.77397
	Target:  5'- gGUcAGUCGA-CGCUgcgGAgcggcaACGACACCGg -3' miRNA:   3'- gCA-UCGGCUgGCGAa--CU------UGCUGUGGC- -5'
8906	5'	-54.2	NC_002484.1	+	33027	0.66	0.803288
	Target:  5'- gCGUgAGCgCGGCUGCgaggUGAGCGAagacgaGCUGa -3' miRNA:   3'- -GCA-UCG-GCUGGCGa---ACUUGCUg-----UGGC- -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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