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
13119	5'	-45.5	NC_003401.1	+	30026	0.66	0.999976
	Target:  5'- ---cGCCAcgUCGGuAGUgugaGGCGAc -3' miRNA:   3'- uuuuCGGUuaAGCC-UCAaaugCUGCU- -5'
13119	5'	-45.5	NC_003401.1	+	100996	0.66	0.999971
	Target:  5'- --uGGCUccagguguuguuuggAAUUCGGGGUggucgACGGCGGu -3' miRNA:   3'- uuuUCGG---------------UUAAGCCUCAaa---UGCUGCU- -5'
13119	5'	-45.5	NC_003401.1	+	132475	0.66	0.999967
	Target:  5'- gGAGGGCCGGgagcCGGGGgaggccgGCGGCGc -3' miRNA:   3'- -UUUUCGGUUaa--GCCUCaaa----UGCUGCu -5'
13119	5'	-45.5	NC_003401.1	+	112911	0.66	0.99994
	Target:  5'- --uAGCCcc-UgGGAGUUUAUGAUGGc -3' miRNA:   3'- uuuUCGGuuaAgCCUCAAAUGCUGCU- -5'
13119	5'	-45.5	NC_003401.1	+	40087	0.67	0.999817
	Target:  5'- gGAGAGCCAAUUgcCGGAGUcauggagACcACGGa -3' miRNA:   3'- -UUUUCGGUUAA--GCCUCAaa-----UGcUGCU- -5'
13119	5'	-45.5	NC_003401.1	+	93028	0.67	0.999763
	Target:  5'- aAGAGGCCG---UGGAuGUaUGCGACGGa -3' miRNA:   3'- -UUUUCGGUuaaGCCU-CAaAUGCUGCU- -5'
13119	5'	-45.5	NC_003401.1	+	30095	1.08	0.030365
	Target:  5'- gAAAAGCCAAUUCGGAGUUUACGACGAc -3' miRNA:   3'- -UUUUCGGUUAAGCCUCAAAUGCUGCU- -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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