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
28384	3'	-56.2	NC_005946.1	+	2612	0.66	0.805833
	Target:  5'- aCCUGcgGcaAGGACUGGGaCCuGGGGGAg -3' miRNA:   3'- aGGACuaC--UCCUGGCCCaGG-CUCUUU- -5'
28384	3'	-56.2	NC_005946.1	+	94430	0.66	0.805833
	Target:  5'- cCCUGGUGAGGGCCcugccuuccGGaUCGGGAGc -3' miRNA:   3'- aGGACUACUCCUGGc--------CCaGGCUCUUu -5'
28384	3'	-56.2	NC_005946.1	+	48110	0.67	0.787317
	Target:  5'- ---aGAUGucgGGGGCCaGGGUCCuGAGAAGu -3' miRNA:   3'- aggaCUAC---UCCUGG-CCCAGG-CUCUUU- -5'
28384	3'	-56.2	NC_005946.1	+	49371	0.67	0.768212
	Target:  5'- gUCgggGAcGAGGACCGGGUCgUGAGu-- -3' miRNA:   3'- aGGa--CUaCUCCUGGCCCAG-GCUCuuu -5'
28384	3'	-56.2	NC_005946.1	+	49426	0.71	0.531153
	Target:  5'- cCCUGGaGGGGACgGGGUCCucguagacGGGAGGa -3' miRNA:   3'- aGGACUaCUCCUGgCCCAGG--------CUCUUU- -5'
28384	3'	-56.2	NC_005946.1	+	71769	0.74	0.353555
	Target:  5'- gUCCUGGUGGGGAaggugucucacuccCUGGGgCCGGGAGg -3' miRNA:   3'- -AGGACUACUCCU--------------GGCCCaGGCUCUUu -5'
28384	3'	-56.2	NC_005946.1	+	47257	1.06	0.00271
	Target:  5'- gUCCUGAUGAGGACCGGGUCCGAGAAAc -3' miRNA:   3'- -AGGACUACUCCUGGCCCAGGCUCUUU- -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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