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
32825	3'	-43.7	NC_007346.1	+	211881	0.66	1
	Target:  5'- aCAAAUAUGgCAUGUUUG-CugUGUUu -3' miRNA:   3'- -GUUUGUACgGUAUAAACaGugGCAAu -5'
32825	3'	-43.7	NC_007346.1	+	28264	0.66	1
	Target:  5'- aCAAGCAcGCaaaaCAUAUUUGUgACCGa-- -3' miRNA:   3'- -GUUUGUaCG----GUAUAAACAgUGGCaau -5'
32825	3'	-43.7	NC_007346.1	+	389581	0.66	1
	Target:  5'- cCGAAcCAUGCCuccugUUGUUACUGUa- -3' miRNA:   3'- -GUUU-GUACGGuaua-AACAGUGGCAau -5'
32825	3'	-43.7	NC_007346.1	+	298634	0.67	1
	Target:  5'- ----gAUGCCAgAUUUGUCAUCGc-- -3' miRNA:   3'- guuugUACGGUaUAAACAGUGGCaau -5'
32825	3'	-43.7	NC_007346.1	+	228067	0.7	1
	Target:  5'- gCAAGCAUGCUAccgUUGuUUACCGUg- -3' miRNA:   3'- -GUUUGUACGGUauaAAC-AGUGGCAau -5'
32825	3'	-43.7	NC_007346.1	+	384931	0.66	1
	Target:  5'- cCAAGCAUGUUAagaggguuacuucUAaUUGUCGCCGa-- -3' miRNA:   3'- -GUUUGUACGGU-------------AUaAACAGUGGCaau -5'
32825	3'	-43.7	NC_007346.1	+	337655	0.7	1
	Target:  5'- aAAACAUGCUcgGUUUGUuCACUGc-- -3' miRNA:   3'- gUUUGUACGGuaUAAACA-GUGGCaau -5'
32825	3'	-43.7	NC_007346.1	+	295509	0.67	1
	Target:  5'- gUAAAC-UGCCGaucggUGUCGCCGUc- -3' miRNA:   3'- -GUUUGuACGGUauaa-ACAGUGGCAau -5'
32825	3'	-43.7	NC_007346.1	+	274006	0.7	0.999999
	Target:  5'- ------cGCCGUAUUUGcCGCCGUg- -3' miRNA:   3'- guuuguaCGGUAUAAACaGUGGCAau -5'
32825	3'	-43.7	NC_007346.1	+	257707	0.72	0.999995
	Target:  5'- aCGGACGgcaccgcccgcguuuUGCCAUAUUccgguaugccgGUCACCGUUAc -3' miRNA:   3'- -GUUUGU---------------ACGGUAUAAa----------CAGUGGCAAU- -5'
32825	3'	-43.7	NC_007346.1	+	211457	1.08	0.113236
	Target:  5'- gCAAACAUGCCAUAUUUGUCACCGUUAu -3' miRNA:   3'- -GUUUGUACGGUAUAAACAGUGGCAAU- -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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