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
8198	5'	-55.7	NC_001978.2	+	15589	0.66	0.590425
	Target:  5'- cAGUGGCUcgacucccuuguuggGcGGGGCGCUcacGCGUUCa -3' miRNA:   3'- -UCAUCGAa--------------C-CCCCGCGAagcCGUAAG- -5'
8198	5'	-55.7	NC_001978.2	+	18809	0.67	0.500821
	Target:  5'- --cGGCUuuUGGGuGCGCg-CGGCGUUCc -3' miRNA:   3'- ucaUCGA--ACCCcCGCGaaGCCGUAAG- -5'
8198	5'	-55.7	NC_001978.2	+	8981	0.67	0.489082
	Target:  5'- gAGgGGCUUgcccuugcugcGGGuGGCGCUaucgccgUCGGCAUUg -3' miRNA:   3'- -UCaUCGAA-----------CCC-CCGCGA-------AGCCGUAAg -5'
8198	5'	-55.7	NC_001978.2	+	21978	0.68	0.448562
	Target:  5'- -uUGGCUUGccacGGGGCaaggaaguuuuGCUUCGGCAg-- -3' miRNA:   3'- ucAUCGAAC----CCCCG-----------CGAAGCCGUaag -5'
8198	5'	-55.7	NC_001978.2	+	16551	0.73	0.203991
	Target:  5'- cGUGGUUgGGGcGGCGUUUCGGCugaccgAUUCa -3' miRNA:   3'- uCAUCGAaCCC-CCGCGAAGCCG------UAAG- -5'
8198	5'	-55.7	NC_001978.2	+	32029	0.75	0.149849
	Target:  5'- --aGGCUgagcGGGGGCGCgucgUCGGC-UUCg -3' miRNA:   3'- ucaUCGAa---CCCCCGCGa---AGCCGuAAG- -5'
8198	5'	-55.7	NC_001978.2	+	27526	1.09	0.000531
	Target:  5'- gAGUAGCUUGGGGGCGCUUCGGCAUUCc -3' miRNA:   3'- -UCAUCGAACCCCCGCGAAGCCGUAAG- -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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