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
19707	3'	-52	NC_004686.1	+	34047	0.66	0.852247
	Target:  5'- --gGCAUCGagGCCGGUGauGAcagcggugccGCCGAGg -3' miRNA:   3'- uaaUGUAGCagUGGCCAC--CU----------UGGCUU- -5'
19707	3'	-52	NC_004686.1	+	41189	0.66	0.852246
	Target:  5'- --aGgAUCG-CGCUGGUGGAAcucCCGGAg -3' miRNA:   3'- uaaUgUAGCaGUGGCCACCUU---GGCUU- -5'
19707	3'	-52	NC_004686.1	+	23578	0.67	0.795714
	Target:  5'- -gUGCAUCGUCcaccaccuggGCUGGUGucACCGGu -3' miRNA:   3'- uaAUGUAGCAG----------UGGCCACcuUGGCUu -5'
19707	3'	-52	NC_004686.1	+	33721	0.67	0.785586
	Target:  5'- ---uCAUCGcCGCCGGggcGGGGCUGAu -3' miRNA:   3'- uaauGUAGCaGUGGCCa--CCUUGGCUu -5'
19707	3'	-52	NC_004686.1	+	16589	0.69	0.699474
	Target:  5'- --gGCGaUGUCGCCGGUGGuccAACCGu- -3' miRNA:   3'- uaaUGUaGCAGUGGCCACC---UUGGCuu -5'
19707	3'	-52	NC_004686.1	+	27253	0.69	0.699473
	Target:  5'- -aUugAggGUcCACCGGUGGAuCCGAAc -3' miRNA:   3'- uaAugUagCA-GUGGCCACCUuGGCUU- -5'
19707	3'	-52	NC_004686.1	+	22502	0.7	0.654331
	Target:  5'- ------cCGUCACCGGUGGGcaGCCuGAAg -3' miRNA:   3'- uaauguaGCAGUGGCCACCU--UGG-CUU- -5'
19707	3'	-52	NC_004686.1	+	35584	0.71	0.58617
	Target:  5'- --cACAagCGUC-UCGGUGGAACCGGu -3' miRNA:   3'- uaaUGUa-GCAGuGGCCACCUUGGCUu -5'
19707	3'	-52	NC_004686.1	+	13380	0.71	0.563671
	Target:  5'- -aUGgGUUGUCACCGGcGGAACCc-- -3' miRNA:   3'- uaAUgUAGCAGUGGCCaCCUUGGcuu -5'
19707	3'	-52	NC_004686.1	+	4140	0.72	0.497845
	Target:  5'- ------gCGUUGCCGGUGGAGCCGu- -3' miRNA:   3'- uaauguaGCAGUGGCCACCUUGGCuu -5'
19707	3'	-52	NC_004686.1	+	44843	1.04	0.004301
	Target:  5'- cAUUACAUCGUCACCGGUGGAACCGAAc -3' miRNA:   3'- -UAAUGUAGCAGUGGCCACCUUGGCUU- -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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