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
11922	3'	-59.8	NC_003278.1	+	19013	0.66	0.350021
	Target:  5'- uGGCCUcgGGCUCGGugauGGucggcuggcugauGCGCGGcAGGAUUu -3' miRNA:   3'- -CCGGA--CCGAGCU----CC-------------CGCGCC-UCUUAG- -5'
11922	3'	-59.8	NC_003278.1	+	33164	0.67	0.295454
	Target:  5'- cGGCCUGaGCgacagCGAcuGGCGCGaGcGGAUCg -3' miRNA:   3'- -CCGGAC-CGa----GCUc-CCGCGC-CuCUUAG- -5'
11922	3'	-59.8	NC_003278.1	+	30097	0.67	0.288118
	Target:  5'- cGGCCUGGCUCucgcGGGUGauuucCGGGcGAAUg -3' miRNA:   3'- -CCGGACCGAGcu--CCCGC-----GCCU-CUUAg -5'
11922	3'	-59.8	NC_003278.1	+	7042	0.7	0.183532
	Target:  5'- aGGaCCUGGCagaUCGgccccgagccggcGGGGCGCGGGGuacgcucGGUCa -3' miRNA:   3'- -CC-GGACCG---AGC-------------UCCCGCGCCUC-------UUAG- -5'
11922	3'	-59.8	NC_003278.1	+	22307	0.71	0.159685
	Target:  5'- cGCUUGaGCUCGAGGGagaacucgauccgcCGCGGGGugccGUCg -3' miRNA:   3'- cCGGAC-CGAGCUCCC--------------GCGCCUCu---UAG- -5'
11922	3'	-59.8	NC_003278.1	+	22140	0.73	0.118539
	Target:  5'- cGGCCUGGCccauggUCGAGGGCacCGGAcGcAUCu -3' miRNA:   3'- -CCGGACCG------AGCUCCCGc-GCCU-CuUAG- -5'
11922	3'	-59.8	NC_003278.1	+	10548	1.11	0.00013
	Target:  5'- gGGCCUGGCUCGAGGGCGCGGAGAAUCg -3' miRNA:   3'- -CCGGACCGAGCUCCCGCGCCUCUUAG- -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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