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
6258	5'	-57.2	NC_001844.1	+	143329	0.66	0.880411
	Target:  5'- cUCCAGGgGC--UCGGAG-CGCCGCUu -3' miRNA:   3'- cAGGUUCaCGcaGGCCUCuGUGGCGG- -5'
6258	5'	-57.2	NC_001844.1	+	136467	0.66	0.879711
	Target:  5'- cGUCagcGGUGCGcgcuaugUCCGcGGAUGCCGCUg -3' miRNA:   3'- -CAGgu-UCACGC-------AGGCcUCUGUGGCGG- -5'
6258	5'	-57.2	NC_001844.1	+	134186	0.66	0.842903
	Target:  5'- gGUCUAugaaGCGgcUCCGGAGACGCCuCUg -3' miRNA:   3'- -CAGGUuca-CGC--AGGCCUCUGUGGcGG- -5'
6258	5'	-57.2	NC_001844.1	+	140849	0.67	0.834815
	Target:  5'- -gCCGGGgaagGCGgCgGGAuGACuACCGCCg -3' miRNA:   3'- caGGUUCa---CGCaGgCCU-CUG-UGGCGG- -5'
6258	5'	-57.2	NC_001844.1	+	116497	0.69	0.715214
	Target:  5'- -cCCAAGUcuGCGUuggCCGGGGccucuaagcgcaaGCGCUGCCa -3' miRNA:   3'- caGGUUCA--CGCA---GGCCUC-------------UGUGGCGG- -5'
6258	5'	-57.2	NC_001844.1	+	19552	0.7	0.676414
	Target:  5'- cUCCGcaagcGUGC-UCCGGGGGCGCauauaGCCg -3' miRNA:   3'- cAGGUu----CACGcAGGCCUCUGUGg----CGG- -5'
6258	5'	-57.2	NC_001844.1	+	101419	0.7	0.666359
	Target:  5'- -gCCA---GCGagCCGGAuGGCACCGCCa -3' miRNA:   3'- caGGUucaCGCa-GGCCU-CUGUGGCGG- -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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