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
22065	3'	-55.7	NC_004927.1	+	36637	0.66	0.7864
	Target:  5'- aCGUCCACCGUgggaGGccaauuGAAGUCuuCGUCg -3' miRNA:   3'- -GCAGGUGGCAgg--CCau----CUUCAG--GCAG- -5'
22065	3'	-55.7	NC_004927.1	+	35641	0.67	0.747285
	Target:  5'- uCGUCCaccacgACCGUcCCGGUcgcGGAaggaaucuugAGUUCGUCu -3' miRNA:   3'- -GCAGG------UGGCA-GGCCA---UCU----------UCAGGCAG- -5'
22065	3'	-55.7	NC_004927.1	+	17940	0.67	0.747285
	Target:  5'- cCGUCCACgGaagaCCGGcgAGAAGgcUCCGUg -3' miRNA:   3'- -GCAGGUGgCa---GGCCa-UCUUC--AGGCAg -5'
22065	3'	-55.7	NC_004927.1	+	23075	0.67	0.727035
	Target:  5'- aCGUcCCACCGUUCGGg------CCGUCg -3' miRNA:   3'- -GCA-GGUGGCAGGCCaucuucaGGCAG- -5'
22065	3'	-55.7	NC_004927.1	+	29473	0.7	0.587217
	Target:  5'- gCGUCCACuuugucgucgauuuCGUCCGGUGGGuagauugucAG-CCGUUg -3' miRNA:   3'- -GCAGGUG--------------GCAGGCCAUCU---------UCaGGCAG- -5'
22065	3'	-55.7	NC_004927.1	+	23183	0.73	0.394304
	Target:  5'- gCG-CCACCGaCCGGcAGAAGUCCaacaGUCg -3' miRNA:   3'- -GCaGGUGGCaGGCCaUCUUCAGG----CAG- -5'
22065	3'	-55.7	NC_004927.1	+	36571	1.1	0.00148
	Target:  5'- cCGUCCACCGUCCGGUAGAAGUCCGUCu -3' miRNA:   3'- -GCAGGUGGCAGGCCAUCUUCAGGCAG- -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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