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
17759	3'	-43.8	NC_004629.1	+	236974	0.68	1
	Target:  5'- -cGuGUAGUUAaucgauaauAAGAGCAUAugGCCCUc -3' miRNA:   3'- caC-CAUCAAU---------UUCUUGUAUuaCGGGA- -5'
17759	3'	-43.8	NC_004629.1	+	229007	0.66	1
	Target:  5'- --------aAAAGAAUAUAGUGCCCUc -3' miRNA:   3'- caccaucaaUUUCUUGUAUUACGGGA- -5'
17759	3'	-43.8	NC_004629.1	+	8023	0.66	1
	Target:  5'- -gGGUGGUcGAAGAGaaaGAUGCUCa -3' miRNA:   3'- caCCAUCAaUUUCUUguaUUACGGGa -5'
17759	3'	-43.8	NC_004629.1	+	154564	0.66	1
	Target:  5'- cGUGGUGGUgaccagAAAGcAUAUAAUGCa-- -3' miRNA:   3'- -CACCAUCAa-----UUUCuUGUAUUACGgga -5'
17759	3'	-43.8	NC_004629.1	+	183064	0.68	1
	Target:  5'- uUGGU-GUUGcaaccGAACAUGAUGaCCCUa -3' miRNA:   3'- cACCAuCAAUuu---CUUGUAUUAC-GGGA- -5'
17759	3'	-43.8	NC_004629.1	+	194723	0.71	0.999971
	Target:  5'- aUGGUGGUguaugGGAGAAUAUcccAAUGCCg- -3' miRNA:   3'- cACCAUCAa----UUUCUUGUA---UUACGGga -5'
17759	3'	-43.8	NC_004629.1	+	207955	0.75	0.997395
	Target:  5'- -cGcGUGGUUAAAacAACAUAAUGCCCUc -3' miRNA:   3'- caC-CAUCAAUUUc-UUGUAUUACGGGA- -5'
17759	3'	-43.8	NC_004629.1	+	167994	1.09	0.075904
	Target:  5'- uGUGGUAGUUAAAGAACAUAAUGCCCUc -3' miRNA:   3'- -CACCAUCAAUUUCUUGUAUUACGGGA- -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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