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
4385	3'	-59.3	NC_001720.1	+	25771	0.66	0.475737
	Target:  5'- cGAGcGGCGGggCCGgcgccGGCGC---CGCGGg -3' miRNA:   3'- -CUU-CCGCCa-GGCa----CCGCGcaaGCGCC- -5'
4385	3'	-59.3	NC_001720.1	+	21008	0.66	0.446467
	Target:  5'- uAGGGCGGUUCcUGGCaGCcGUUaucuacagccgCGCGGg -3' miRNA:   3'- cUUCCGCCAGGcACCG-CG-CAA-----------GCGCC- -5'
4385	3'	-59.3	NC_001720.1	+	29032	0.67	0.427521
	Target:  5'- gGGAGGCGGUCUGacGGC-UGa-CGCGGa -3' miRNA:   3'- -CUUCCGCCAGGCa-CCGcGCaaGCGCC- -5'
4385	3'	-59.3	NC_001720.1	+	23869	0.67	0.40906
	Target:  5'- cAAGGCGGUaCUGUc-CGCGUaccgaaUCGCGGa -3' miRNA:   3'- cUUCCGCCA-GGCAccGCGCA------AGCGCC- -5'
4385	3'	-59.3	NC_001720.1	+	11914	0.67	0.385817
	Target:  5'- cGgcGGCGGcaaUCCGUuguagggcGGCGCGgcgacguucggcgaUCGCGGc -3' miRNA:   3'- -CuuCCGCC---AGGCA--------CCGCGCa-------------AGCGCC- -5'
4385	3'	-59.3	NC_001720.1	+	22908	0.69	0.287513
	Target:  5'- cGAcGGUGG-CCaUGGCGCGUUgCGCGc -3' miRNA:   3'- -CUuCCGCCaGGcACCGCGCAA-GCGCc -5'
4385	3'	-59.3	NC_001720.1	+	37673	1.09	0.000337
	Target:  5'- aGAAGGCGGUCCGUGGCGCGUUCGCGGu -3' miRNA:   3'- -CUUCCGCCAGGCACCGCGCAAGCGCC- -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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