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
4334	3'	-57.8	NC_001720.1	+	26924	0.66	0.523315
	Target:  5'- uGuuGGAaaucGAGUCguacgccGCCGCCGUCCc -3' miRNA:   3'- -UggCCUgu--CUCAGau-----CGGUGGCAGGc -5'
4334	3'	-57.8	NC_001720.1	+	37184	0.66	0.512838
	Target:  5'- uACCGG-CAGAGUCUcgggguucuGGUC-CCaGUCCu -3' miRNA:   3'- -UGGCCuGUCUCAGA---------UCGGuGG-CAGGc -5'
4334	3'	-57.8	NC_001720.1	+	9879	0.66	0.502448
	Target:  5'- cACCGGAaauGGGUCUggaucaccAGCCGCacUCCGg -3' miRNA:   3'- -UGGCCUgu-CUCAGA--------UCGGUGgcAGGC- -5'
4334	3'	-57.8	NC_001720.1	+	24953	0.67	0.471858
	Target:  5'- gUCGGAC-GAGgaagugCUGGCCAUCGUggacCCGa -3' miRNA:   3'- uGGCCUGuCUCa-----GAUCGGUGGCA----GGC- -5'
4334	3'	-57.8	NC_001720.1	+	4244	0.7	0.311662
	Target:  5'- cCCGGACAGAGcCUcauuaaccAGUUACCcUCCGa -3' miRNA:   3'- uGGCCUGUCUCaGA--------UCGGUGGcAGGC- -5'
4334	3'	-57.8	NC_001720.1	+	22151	0.72	0.218185
	Target:  5'- gUCGGGCGGAG-CaGGCCGCgGUCUGa -3' miRNA:   3'- uGGCCUGUCUCaGaUCGGUGgCAGGC- -5'
4334	3'	-57.8	NC_001720.1	+	12163	1.07	0.0006
	Target:  5'- cACCGGACAGAGUCUAGCCACCGUCCGc -3' miRNA:   3'- -UGGCCUGUCUCAGAUCGGUGGCAGGC- -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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