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
23535	3'	-45	NC_005260.1	+	3014	0.66	1
	Target:  5'- aGAaguuuAUCAAGUUUAUCGAuguCAAGUUc -3' miRNA:   3'- gCUgc---UAGUUCGAAUAGCUu--GUUCAA- -5'
23535	3'	-45	NC_005260.1	+	31579	0.68	0.999993
	Target:  5'- aGACGAUCAAGUUaGUUGGucaaagggauuCAAGUUa -3' miRNA:   3'- gCUGCUAGUUCGAaUAGCUu----------GUUCAA- -5'
23535	3'	-45	NC_005260.1	+	103119	0.68	0.99999
	Target:  5'- -uAUGAUCAAGCguaugAUCGAugAAGa- -3' miRNA:   3'- gcUGCUAGUUCGaa---UAGCUugUUCaa -5'
23535	3'	-45	NC_005260.1	+	4607	0.68	0.999989
	Target:  5'- cCGAUGAUCAAGCgucagcacaagAUCGAaaucaacaaaGCAAGa- -3' miRNA:   3'- -GCUGCUAGUUCGaa---------UAGCU----------UGUUCaa -5'
23535	3'	-45	NC_005260.1	+	74938	0.68	0.999986
	Target:  5'- aGAaGAUCAGGCgcuagaUGUUGAACAGGa- -3' miRNA:   3'- gCUgCUAGUUCGa-----AUAGCUUGUUCaa -5'
23535	3'	-45	NC_005260.1	+	168651	0.69	0.999973
	Target:  5'- uCGGCGAUC-AGCg---CGAuuACAAGUUg -3' miRNA:   3'- -GCUGCUAGuUCGaauaGCU--UGUUCAA- -5'
23535	3'	-45	NC_005260.1	+	201705	0.7	0.999886
	Target:  5'- gCGACGGcaAAGCUUggAUCGAugAAGUc -3' miRNA:   3'- -GCUGCUagUUCGAA--UAGCUugUUCAa -5'
23535	3'	-45	NC_005260.1	+	179500	0.71	0.999755
	Target:  5'- aGACGAUCAAGaCUUG-CGAGUGAGUc -3' miRNA:   3'- gCUGCUAGUUC-GAAUaGCUUGUUCAa -5'
23535	3'	-45	NC_005260.1	+	7949	0.71	0.999755
	Target:  5'- -aGCGAUCAAGCaugUAUUGAACAAc-- -3' miRNA:   3'- gcUGCUAGUUCGa--AUAGCUUGUUcaa -5'
23535	3'	-45	NC_005260.1	+	16915	0.79	0.93897
	Target:  5'- uGAUGAUCAAGCUUAUCGc-CGAGa- -3' miRNA:   3'- gCUGCUAGUUCGAAUAGCuuGUUCaa -5'
23535	3'	-45	NC_005260.1	+	87252	1.08	0.055736
	Target:  5'- aCGACGAUCAAGCUUAUCGAACAAGUUa -3' miRNA:   3'- -GCUGCUAGUUCGAAUAGCUUGUUCAA- -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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