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
18415	5'	-59.5	NC_004681.1	+	65498	0.66	0.527396
	Target:  5'- aCUUCUGG-GUGuGCGCGGGCaCCGGAu -3' miRNA:   3'- -GGGGACCaCACcCGUGUCUG-GGUCUu -5'
18415	5'	-59.5	NC_004681.1	+	50370	0.66	0.527396
	Target:  5'- gCCCUucuugcgGUGGGCGCGGGaCCAGGAc -3' miRNA:   3'- gGGGAcca----CACCCGUGUCUgGGUCUU- -5'
18415	5'	-59.5	NC_004681.1	+	58768	0.68	0.429195
	Target:  5'- cCCCCgaUGGUGUcacgcgcaccgucGaGGCGCGcGCCCAGGAg -3' miRNA:   3'- -GGGG--ACCACA-------------C-CCGUGUcUGGGUCUU- -5'
18415	5'	-59.5	NC_004681.1	+	43918	0.71	0.291796
	Target:  5'- aCgCUGGUgccguagcggggGUGGGCGCGGACCUcguGGAAg -3' miRNA:   3'- gGgGACCA------------CACCCGUGUCUGGG---UCUU- -5'
18415	5'	-59.5	NC_004681.1	+	44799	0.71	0.284841
	Target:  5'- gCCCUGGagGUGGGCA-AGACCUAcGAc -3' miRNA:   3'- gGGGACCa-CACCCGUgUCUGGGU-CUu -5'
18415	5'	-59.5	NC_004681.1	+	18216	0.71	0.284841
	Target:  5'- cCCCCgGGUGUaccGGGCggGCAGACUCcGAAa -3' miRNA:   3'- -GGGGaCCACA---CCCG--UGUCUGGGuCUU- -5'
18415	5'	-59.5	NC_004681.1	+	22705	1.07	0.000716
	Target:  5'- cCCCCUGGUGUGGGCACAGACCCAGAAc -3' miRNA:   3'- -GGGGACCACACCCGUGUCUGGGUCUU- -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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