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
382	3'	-54.9	AC_000011.1	+	25513	0.67	0.579396
	Target:  5'- gCUCCUCaccggUC-UGggGGUCgagguagaccCCGCGGc -3' miRNA:   3'- aGAGGAGg----AGaACuuCCAGa---------GGCGCC- -5'
382	3'	-54.9	AC_000011.1	+	11329	0.68	0.523242
	Target:  5'- cUCUCCUCCuucacggUCUgcucguacgccgUGAccAGGUUggCCGCGGc -3' miRNA:   3'- -AGAGGAGG-------AGA------------ACU--UCCAGa-GGCGCC- -5'
382	3'	-54.9	AC_000011.1	+	23172	0.68	0.502841
	Target:  5'- aUCUCUUCCUCUUcuuGGUCcgaggccaCGCGGc -3' miRNA:   3'- -AGAGGAGGAGAAcuuCCAGag------GCGCC- -5'
382	3'	-54.9	AC_000011.1	+	2191	0.72	0.323207
	Target:  5'- cCUCCUCCUCcgccgGAGGGUCcaggCCGgcucuCGGg -3' miRNA:   3'- aGAGGAGGAGaa---CUUCCAGa---GGC-----GCC- -5'
382	3'	-54.9	AC_000011.1	+	23606	0.73	0.284609
	Target:  5'- gCUCCUCCUCgug-----CUCCGCGGg -3' miRNA:   3'- aGAGGAGGAGaacuuccaGAGGCGCC- -5'
382	3'	-54.9	AC_000011.1	+	24525	0.76	0.16136
	Target:  5'- uUCUCCUCgacCUUGcgcAGGGUCUCCGCGu -3' miRNA:   3'- -AGAGGAGga-GAAC---UUCCAGAGGCGCc -5'
382	3'	-54.9	AC_000011.1	+	8766	1.1	0.000571
	Target:  5'- aUCUCCUCCUCUUGAAGGUCUCCGCGGc -3' miRNA:   3'- -AGAGGAGGAGAACUUCCAGAGGCGCC- -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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