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
21293	5'	-53.4	NC_004778.3	+	121564	0.66	0.9471
	Target:  5'- --cGAcGCGUGCCUGCUgcucagCCGCa--- -3' miRNA:   3'- acaCUuUGUACGGACGGa-----GGCGcuac -5'
21293	5'	-53.4	NC_004778.3	+	96587	0.66	0.942479
	Target:  5'- cGUGGAGCAcccUGCUaGCCagCGCGGc- -3' miRNA:   3'- aCACUUUGU---ACGGaCGGagGCGCUac -5'
21293	5'	-53.4	NC_004778.3	+	126214	0.66	0.937604
	Target:  5'- cGUGGAACGUuugaaauccgaGCUgGCCUCaaaaucaGCGGUGa -3' miRNA:   3'- aCACUUUGUA-----------CGGaCGGAGg------CGCUAC- -5'
21293	5'	-53.4	NC_004778.3	+	123824	0.66	0.937604
	Target:  5'- uUGUGGAACuuuUGCCgacgaggGCUgUUCGCGAUa -3' miRNA:   3'- -ACACUUUGu--ACGGa------CGG-AGGCGCUAc -5'
21293	5'	-53.4	NC_004778.3	+	126380	0.68	0.859309
	Target:  5'- gGUGccGCAUGUgUGCCUugCCGCGuUGa -3' miRNA:   3'- aCACuuUGUACGgACGGA--GGCGCuAC- -5'
21293	5'	-53.4	NC_004778.3	+	6283	0.73	0.645983
	Target:  5'- cGUGAGua--GCCUGCCUCUGCauaaGAUGg -3' miRNA:   3'- aCACUUuguaCGGACGGAGGCG----CUAC- -5'
21293	5'	-53.4	NC_004778.3	+	29260	1.08	0.004396
	Target:  5'- gUGUGAAACAUGCCUGCCUCCGCGAUGc -3' miRNA:   3'- -ACACUUUGUACGGACGGAGGCGCUAC- -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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