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
91	5'	-57.8	AC_000006.1	+	7494	0.66	0.474722
	Target:  5'- cGCGGGCCaUGAGGgUCUGGAgcucgucgcgaaAGaGGCGg -3' miRNA:   3'- -CGCCUGGgACUCUgGGACCU------------UC-CUGU- -5'
91	5'	-57.8	AC_000006.1	+	17144	0.66	0.434631
	Target:  5'- cCGGACCUaUGGGAacaaggCCUGGAauaguagcacGGGGCAg -3' miRNA:   3'- cGCCUGGG-ACUCUg-----GGACCU----------UCCUGU- -5'
91	5'	-57.8	AC_000006.1	+	18546	0.66	0.434631
	Target:  5'- cGCGGuaGCCCggcgucGGGAUaaUGGAAGGAUg -3' miRNA:   3'- -CGCC--UGGGa-----CUCUGggACCUUCCUGu -5'
91	5'	-57.8	AC_000006.1	+	8000	0.66	0.424917
	Target:  5'- cGUGGgacucACCCUGGGGCuCCUcGA-GGACGg -3' miRNA:   3'- -CGCC-----UGGGACUCUG-GGAcCUuCCUGU- -5'
91	5'	-57.8	AC_000006.1	+	23615	0.67	0.396571
	Target:  5'- cCGcGACCCccAGGCCCUGGAgcAGcGGCGc -3' miRNA:   3'- cGC-CUGGGacUCUGGGACCU--UC-CUGU- -5'
91	5'	-57.8	AC_000006.1	+	2793	0.71	0.216472
	Target:  5'- cUGGACUgUGAGGCCCgcuUGGAugacuuuucagAGGACGg -3' miRNA:   3'- cGCCUGGgACUCUGGG---ACCU-----------UCCUGU- -5'
91	5'	-57.8	AC_000006.1	+	29956	1.1	0.000257
	Target:  5'- cGCGGACCCUGAGACCCUGGAAGGACAu -3' miRNA:   3'- -CGCCUGGGACUCUGGGACCUUCCUGU- -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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