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
11460	3'	-53.8	NC_003085.1	+	44569	0.66	0.764049
	Target:  5'- gACUGCGUCUcaaGGAGGGGAcg-UCAGg -3' miRNA:   3'- -UGGUGCAGGca-CCUCUCCUugaAGUC- -5'
11460	3'	-53.8	NC_003085.1	+	36071	0.67	0.710774
	Target:  5'- gUCAUGUCCGUGGccGAcGAACUUCu- -3' miRNA:   3'- uGGUGCAGGCACCu-CUcCUUGAAGuc -5'
11460	3'	-53.8	NC_003085.1	+	7848	0.67	0.698733
	Target:  5'- gGCCAUGUUCGaGGAGAagcgcgcggaacuGGGGCUUgAGc -3' miRNA:   3'- -UGGUGCAGGCaCCUCU-------------CCUUGAAgUC- -5'
11460	3'	-53.8	NC_003085.1	+	30150	0.68	0.6555
	Target:  5'- gGCCccCGUCaacuccagGGAGAGGAGCUUCu- -3' miRNA:   3'- -UGGu-GCAGgca-----CCUCUCCUUGAAGuc -5'
11460	3'	-53.8	NC_003085.1	+	28206	0.69	0.566411
	Target:  5'- cACCACcuuGUCCGUcGuccaguucgccaAGAGGGGCUUCGGa -3' miRNA:   3'- -UGGUG---CAGGCAcC------------UCUCCUUGAAGUC- -5'
11460	3'	-53.8	NC_003085.1	+	23238	0.71	0.470426
	Target:  5'- cACCAUaUCC-UGGccGAGGGACUUCAGg -3' miRNA:   3'- -UGGUGcAGGcACCu-CUCCUUGAAGUC- -5'
11460	3'	-53.8	NC_003085.1	+	24784	1.09	0.001213
	Target:  5'- cACCACGUCCGUGGAGAGGAACUUCAGg -3' miRNA:   3'- -UGGUGCAGGCACCUCUCCUUGAAGUC- -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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