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
21168	3'	-55.1	NC_004777.1	+	29810	0.69	0.383391
	Target:  5'- -uGCAGUCugguGCCUCAGG-GAAGUUc -3' miRNA:   3'- guCGUCGGuau-CGGAGUCCaCUUCGG- -5'
21168	3'	-55.1	NC_004777.1	+	25021	0.78	0.093469
	Target:  5'- cCAGCAGCCuUAGCUUCAagaaugucauGGUG-AGCCg -3' miRNA:   3'- -GUCGUCGGuAUCGGAGU----------CCACuUCGG- -5'
21168	3'	-55.1	NC_004777.1	+	21185	0.68	0.421863
	Target:  5'- aAGCAGCacgAGCCUUAGucaGAGCCg -3' miRNA:   3'- gUCGUCGguaUCGGAGUCcacUUCGG- -5'
21168	3'	-55.1	NC_004777.1	+	20910	0.67	0.494409
	Target:  5'- uCAGCAGUCAggaGGCCaUCAauGGUGAuGaCCu -3' miRNA:   3'- -GUCGUCGGUa--UCGG-AGU--CCACUuC-GG- -5'
21168	3'	-55.1	NC_004777.1	+	20409	0.66	0.583506
	Target:  5'- aCGGUccgaaaAGCCuucacgcuugGUAGCCUgAGGUuuAGCCg -3' miRNA:   3'- -GUCG------UCGG----------UAUCGGAgUCCAcuUCGG- -5'
21168	3'	-55.1	NC_004777.1	+	19458	1.12	0.000292
	Target:  5'- gCAGCAGCCAUAGCCUCAGGUGAAGCCg -3' miRNA:   3'- -GUCGUCGGUAUCGGAGUCCACUUCGG- -5'
21168	3'	-55.1	NC_004777.1	+	2578	0.66	0.580086
	Target:  5'- gCAGCAGCaCGUuuccaugcggugagAGCCUCAGGauucguGUCg -3' miRNA:   3'- -GUCGUCG-GUA--------------UCGGAGUCCacuu--CGG- -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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