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
2385	5'	-50.2	NC_001416.1	+	1954	0.71	0.677021
	Target:  5'- gCCGGGugaGGAAAGCUGGCUGaUUGAc-- -3' miRNA:   3'- -GGCCUg--CCUUUCGACUGGC-GAUUuuu -5'
2385	5'	-50.2	NC_001416.1	+	2352	0.68	0.836486
	Target:  5'- cCCGGAUauuuuugaucugaccGAAgcgcagcAGCUGACUGCUGAAGAg -3' miRNA:   3'- -GGCCUGc--------------CUU-------UCGACUGGCGAUUUUU- -5'
2385	5'	-50.2	NC_001416.1	+	3455	0.68	0.845672
	Target:  5'- -aGGACGGGuauccuGGCUGgauGCCGCaGAAAu -3' miRNA:   3'- ggCCUGCCUu-----UCGAC---UGGCGaUUUUu -5'
2385	5'	-50.2	NC_001416.1	+	3734	0.69	0.755436
	Target:  5'- -aGGagcaGCGGGAaaGGCUGACCgGCUGGAu- -3' miRNA:   3'- ggCC----UGCCUU--UCGACUGG-CGAUUUuu -5'
2385	5'	-50.2	NC_001416.1	+	4691	0.66	0.922598
	Target:  5'- gCCGGACGcGGgcGCUGcaGCCGUa----- -3' miRNA:   3'- -GGCCUGC-CUuuCGAC--UGGCGauuuuu -5'
2385	5'	-50.2	NC_001416.1	+	18336	1.09	0.002703
	Target:  5'- aCCGGACGGAAAGCUGACCGCUAAAAAu -3' miRNA:   3'- -GGCCUGCCUUUCGACUGGCGAUUUUU- -5'
2385	5'	-50.2	NC_001416.1	+	20157	0.66	0.916221
	Target:  5'- uCCGG-CGGAcguGCUGGCgGCg----- -3' miRNA:   3'- -GGCCuGCCUuu-CGACUGgCGauuuuu -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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