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
21274	3'	-56.1	NC_004778.3	+	68254	0.66	0.869994
	Target:  5'- --gGUGGAUGcUGcgUCGCUGGCgcucGGGCu -3' miRNA:   3'- uugCACUUAC-ACa-AGCGGCCG----CCCGu -5'
21274	3'	-56.1	NC_004778.3	+	85562	0.66	0.854511
	Target:  5'- cGCGUGGGcgacGUGUacggcgUCGCCcacGCGGGCGu -3' miRNA:   3'- uUGCACUUa---CACA------AGCGGc--CGCCCGU- -5'
21274	3'	-56.1	NC_004778.3	+	21175	0.67	0.812273
	Target:  5'- uGCGUaGggUuaaaGUGcUCGCCGGCGGacguGCAg -3' miRNA:   3'- uUGCA-CuuA----CACaAGCGGCCGCC----CGU- -5'
21274	3'	-56.1	NC_004778.3	+	62286	0.68	0.77538
	Target:  5'- cGCGguaauUGAGgaccUGUUCGCCGGCGgcGGCAc -3' miRNA:   3'- uUGC-----ACUUac--ACAAGCGGCCGC--CCGU- -5'
21274	3'	-56.1	NC_004778.3	+	90768	0.7	0.633558
	Target:  5'- cAACGUGuuUcUGUUUGCCGGCGGuCAc -3' miRNA:   3'- -UUGCACuuAcACAAGCGGCCGCCcGU- -5'
21274	3'	-56.1	NC_004778.3	+	121698	0.72	0.510458
	Target:  5'- cGGCGUGGGcGUGUugcUgGCCGGCGGcGCu -3' miRNA:   3'- -UUGCACUUaCACA---AgCGGCCGCC-CGu -5'
21274	3'	-56.1	NC_004778.3	+	4036	1.06	0.003164
	Target:  5'- aAACGUGAAUGUGUUCGCCGGCGGGCAg -3' miRNA:   3'- -UUGCACUUACACAAGCGGCCGCCCGU- -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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