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
21989	3'	-59.5	NC_004914.1	+	19564	0.67	0.447633
	Target:  5'- aUGaUUCUGC-GGUCUGGGuGGCGAAg -3' miRNA:   3'- gACcAGGACGuCCAGGCUCuCCGCUU- -5'
21989	3'	-59.5	NC_004914.1	+	5083	0.67	0.444767
	Target:  5'- aCUGGUCCUGCAGGUcauuaaaguacgucCCcAGAaGCGu- -3' miRNA:   3'- -GACCAGGACGUCCA--------------GGcUCUcCGCuu -5'
21989	3'	-59.5	NC_004914.1	+	11735	0.68	0.398569
	Target:  5'- uCUGGUUCcaaaaucccuucaaUGCAGGcgugUCUGAGcAGGCGGAg -3' miRNA:   3'- -GACCAGG--------------ACGUCC----AGGCUC-UCCGCUU- -5'
21989	3'	-59.5	NC_004914.1	+	8954	0.68	0.392351
	Target:  5'- -aGGUCCUGCAGGcCCGcaAGGUc-- -3' miRNA:   3'- gaCCAGGACGUCCaGGCucUCCGcuu -5'
21989	3'	-59.5	NC_004914.1	+	9586	0.68	0.392351
	Target:  5'- -aGGUgCgGCAGGcCCGguGGGGGCGAc -3' miRNA:   3'- gaCCAgGaCGUCCaGGC--UCUCCGCUu -5'
21989	3'	-59.5	NC_004914.1	+	8807	0.68	0.366425
	Target:  5'- -aGGgCCUGCuGGUCCGcGuGGUGAGa -3' miRNA:   3'- gaCCaGGACGuCCAGGCuCuCCGCUU- -5'
21989	3'	-59.5	NC_004914.1	+	9440	0.77	0.087525
	Target:  5'- gCUGGUCCgGCAGGcCCGcAGGGGcCGAAa -3' miRNA:   3'- -GACCAGGaCGUCCaGGC-UCUCC-GCUU- -5'
21989	3'	-59.5	NC_004914.1	+	9059	1.05	0.000719
	Target:  5'- cCUGGUCCUGCAGGUCCGAGAGGCGAAc -3' miRNA:   3'- -GACCAGGACGUCCAGGCUCUCCGCUU- -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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