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
21187	3'	-49.6	NC_004778.3	+	45411	0.66	0.994779
	Target:  5'- uGUCGcUGaUGCuguuaguuUUGCUGGCgCGGCg -3' miRNA:   3'- uCAGCuAUaACGu-------AAUGACCGgGCUG- -5'
21187	3'	-49.6	NC_004778.3	+	115191	0.67	0.984168
	Target:  5'- cGGUCGAacaggaUGUUGCGaucgcuUUGGCCgGGCa -3' miRNA:   3'- -UCAGCU------AUAACGUaau---GACCGGgCUG- -5'
21187	3'	-49.6	NC_004778.3	+	48964	0.69	0.954151
	Target:  5'- gGGUCGAUGcgcUGCcagcgcacguacAUcacgaACUGGCCCGACc -3' miRNA:   3'- -UCAGCUAUa--ACG------------UAa----UGACCGGGCUG- -5'
21187	3'	-49.6	NC_004778.3	+	48393	0.7	0.935289
	Target:  5'- cAGuUUGGUGUaGUucUUGCUGGCCCGAa -3' miRNA:   3'- -UC-AGCUAUAaCGu-AAUGACCGGGCUg -5'
21187	3'	-49.6	NC_004778.3	+	49562	0.71	0.918316
	Target:  5'- cGUCGcggaagcacuuGUAUUGCcuagcgACUGGCaCCGACa -3' miRNA:   3'- uCAGC-----------UAUAACGuaa---UGACCG-GGCUG- -5'
21187	3'	-49.6	NC_004778.3	+	6393	0.77	0.631936
	Target:  5'- cGUCGuaaaacGCGUUGCUGGCCCGcCg -3' miRNA:   3'- uCAGCuauaa-CGUAAUGACCGGGCuG- -5'
21187	3'	-49.6	NC_004778.3	+	121843	1.11	0.00646
	Target:  5'- aAGUCGAUAUUGCAUUACUGGCCCGACg -3' miRNA:   3'- -UCAGCUAUAACGUAAUGACCGGGCUG- -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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