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
6212	3'	-55.2	NC_001844.1	+	61208	0.66	0.898372
	Target:  5'- -uGCCgcuagcGCAGCG-CUGUgcGCCGUUGg -3' miRNA:   3'- uuUGGa-----CGUCGCuGACGa-CGGCAACg -5'
6212	3'	-55.2	NC_001844.1	+	116508	0.67	0.869858
	Target:  5'- aGGACCaGCGGCccaaguCUGCguugGCCGggGCc -3' miRNA:   3'- -UUUGGaCGUCGcu----GACGa---CGGCaaCG- -5'
6212	3'	-55.2	NC_001844.1	+	58295	0.67	0.854226
	Target:  5'- -uGCCUGCcugaaacacGCGGUUGUUGCCGgcGCu -3' miRNA:   3'- uuUGGACGu--------CGCUGACGACGGCaaCG- -5'
6212	3'	-55.2	NC_001844.1	+	142206	0.68	0.782873
	Target:  5'- -----aGCGGCGGCUcauggccaccgagGCUGCCGcgUGCg -3' miRNA:   3'- uuuggaCGUCGCUGA-------------CGACGGCa-ACG- -5'
6212	3'	-55.2	NC_001844.1	+	113528	0.71	0.631045
	Target:  5'- -cGCCUGCGGaCGGCgcGgaGCCGggGCc -3' miRNA:   3'- uuUGGACGUC-GCUGa-CgaCGGCaaCG- -5'
6212	3'	-55.2	NC_001844.1	+	3927	0.71	0.620519
	Target:  5'- gGGugCUacaGCAGCGACUGCaaGCUGggGCu -3' miRNA:   3'- -UUugGA---CGUCGCUGACGa-CGGCaaCG- -5'
6212	3'	-55.2	NC_001844.1	+	68972	1.1	0.00218
	Target:  5'- uAAACCUGCAGCGACUGCUGCCGUUGCg -3' miRNA:   3'- -UUUGGACGUCGCUGACGACGGCAACG- -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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