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
19272	3'	-51.3	NC_004685.1	+	36481	0.66	0.937772
	Target:  5'- gGGAUgAUccgacGCCUGACUUCGcGUCGu- -3' miRNA:   3'- aCCUAgUA-----CGGACUGGAGCuUAGUgu -5'
19272	3'	-51.3	NC_004685.1	+	16634	0.66	0.926666
	Target:  5'- gGGAUCGUGCCgaccaacgUGACCgaggacgacaUCGAccCGCGc -3' miRNA:   3'- aCCUAGUACGG--------ACUGG----------AGCUuaGUGU- -5'
19272	3'	-51.3	NC_004685.1	+	9546	0.66	0.920683
	Target:  5'- cGGAUCGU-CCUGGCCgCGcccCGCAa -3' miRNA:   3'- aCCUAGUAcGGACUGGaGCuuaGUGU- -5'
19272	3'	-51.3	NC_004685.1	+	7720	0.67	0.901023
	Target:  5'- aGGcgUGUGCCUGugCggCGAGgccCGCAg -3' miRNA:   3'- aCCuaGUACGGACugGa-GCUUa--GUGU- -5'
19272	3'	-51.3	NC_004685.1	+	65347	0.68	0.85432
	Target:  5'- gGGAccUCgAUGCgCUGGCCcccgacgCGGAUCACGa -3' miRNA:   3'- aCCU--AG-UACG-GACUGGa------GCUUAGUGU- -5'
19272	3'	-51.3	NC_004685.1	+	29719	0.68	0.836743
	Target:  5'- aGGGUCAggGUCUGGCC-CGAggugcgGUCGCc -3' miRNA:   3'- aCCUAGUa-CGGACUGGaGCU------UAGUGu -5'
19272	3'	-51.3	NC_004685.1	+	59541	0.69	0.798992
	Target:  5'- cGGG--GUGCCUGccaGCCcgUCGggUCGCAg -3' miRNA:   3'- aCCUagUACGGAC---UGG--AGCuuAGUGU- -5'
19272	3'	-51.3	NC_004685.1	+	66990	1.09	0.003099
	Target:  5'- gUGGAUCAUGCCUGACCUCGAAUCACAc -3' miRNA:   3'- -ACCUAGUACGGACUGGAGCUUAGUGU- -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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