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
113	5'	-56	AC_000006.1	+	4547	0.83	0.039741
	Target:  5'- cGGGCcccGggGCGAaGUUCCCCUCGCAGa -3' miRNA:   3'- -CCCG---CuuUGCUaCAAGGGGGGCGUCa -5'
113	5'	-56	AC_000006.1	+	8330	0.74	0.180575
	Target:  5'- cGGCGGcAGCGGcgGUUCCggCCCCGCGGg -3' miRNA:   3'- cCCGCU-UUGCUa-CAAGG--GGGGCGUCa -5'
113	5'	-56	AC_000006.1	+	6541	0.71	0.302752
	Target:  5'- uGGGCuccGAGAagaugcCGAUGUUggugggauaacagcgCCCCCCGCGGa -3' miRNA:   3'- -CCCG---CUUU------GCUACAA---------------GGGGGGCGUCa -5'
113	5'	-56	AC_000006.1	+	5129	0.68	0.440824
	Target:  5'- cGGUGAAGgGGUGggCCCCUgGCuGg -3' miRNA:   3'- cCCGCUUUgCUACaaGGGGGgCGuCa -5'
113	5'	-56	AC_000006.1	+	5750	0.66	0.534958
	Target:  5'- cGGUGGAAaaGGUGgaCCCCCUGguGg -3' miRNA:   3'- cCCGCUUUg-CUACaaGGGGGGCguCa -5'
113	5'	-56	AC_000006.1	+	15263	0.69	0.365584
	Target:  5'- cGGCGGcGGCGGUGgcagUCCgCCCGCGc- -3' miRNA:   3'- cCCGCU-UUGCUACa---AGGgGGGCGUca -5'
113	5'	-56	AC_000006.1	+	24500	0.69	0.365584
	Target:  5'- -aGCGGAGCGGUGga-CUCCUGCGGa -3' miRNA:   3'- ccCGCUUUGCUACaagGGGGGCGUCa -5'
113	5'	-56	AC_000006.1	+	25081	1.09	0.000494
	Target:  5'- cGGGCGAAACGAUGUUCCCCCCGCAGUc -3' miRNA:   3'- -CCCGCUUUGCUACAAGGGGGGCGUCA- -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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