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
28220	3'	-51.2	NC_005891.1	+	37941	0.66	0.8633
	Target:  5'- uUGUUCCCCGU-CGAGUgaACucuauGGaGCg -3' miRNA:   3'- gACGAGGGGCAuGCUUAa-UGuu---CC-CG- -5'
28220	3'	-51.2	NC_005891.1	+	7236	0.66	0.845664
	Target:  5'- uUGUUCCgaaGcGCGAuuggGCGAGGGCg -3' miRNA:   3'- gACGAGGgg-CaUGCUuaa-UGUUCCCG- -5'
28220	3'	-51.2	NC_005891.1	+	18629	0.66	0.817378
	Target:  5'- -aGCUCUgCGUccauGUUACGAGGGUc -3' miRNA:   3'- gaCGAGGgGCAugcuUAAUGUUCCCG- -5'
28220	3'	-51.2	NC_005891.1	+	33363	0.66	0.8164
	Target:  5'- gUGCUCCUaCGaUugGggUUugGuuaguagauugaaAGGGCg -3' miRNA:   3'- gACGAGGG-GC-AugCuuAAugU-------------UCCCG- -5'
28220	3'	-51.2	NC_005891.1	+	227	0.67	0.776711
	Target:  5'- -cGCUCCCCGUAuuCGGA--ACuauGGGa -3' miRNA:   3'- gaCGAGGGGCAU--GCUUaaUGuu-CCCg -5'
28220	3'	-51.2	NC_005891.1	+	16641	0.72	0.502446
	Target:  5'- -cGCUCCCCG-ACGAGUUGaaaccugagacagcCAAGGcuGCg -3' miRNA:   3'- gaCGAGGGGCaUGCUUAAU--------------GUUCC--CG- -5'
28220	3'	-51.2	NC_005891.1	+	18526	1.13	0.000894
	Target:  5'- gCUGCUCCCCGUACGAAUUACAAGGGCa -3' miRNA:   3'- -GACGAGGGGCAUGCUUAAUGUUCCCG- -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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