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
8666	3'	-48.8	NC_002229.2	+	71748	0.66	0.997549
	Target:  5'- gAUGUaGCCCaaaagggCGGAGGUUuUUCCGCAa- -3' miRNA:   3'- -UACAaCGGG-------GUCUUCAA-AAGGUGUau -5'
8666	3'	-48.8	NC_002229.2	+	138346	0.68	0.991351
	Target:  5'- ----cGCCCCAGggGgcg-CCGCGg- -3' miRNA:   3'- uacaaCGGGGUCuuCaaaaGGUGUau -5'
8666	3'	-48.8	NC_002229.2	+	365	0.68	0.991351
	Target:  5'- ----cGCCCCAGggGgcg-CCGCGg- -3' miRNA:   3'- uacaaCGGGGUCuuCaaaaGGUGUau -5'
8666	3'	-48.8	NC_002229.2	+	68939	0.69	0.983306
	Target:  5'- gAUGUgugGCCgCGGAGGUgUUCUAUAUGg -3' miRNA:   3'- -UACAa--CGGgGUCUUCAaAAGGUGUAU- -5'
8666	3'	-48.8	NC_002229.2	+	814	0.71	0.942857
	Target:  5'- -gGUUGCCCCGGggGcg--CCGCu-- -3' miRNA:   3'- uaCAACGGGGUCuuCaaaaGGUGuau -5'
8666	3'	-48.8	NC_002229.2	+	137897	0.71	0.942857
	Target:  5'- -gGUUGCCCCGGggGcg--CCGCu-- -3' miRNA:   3'- uaCAACGGGGUCuuCaaaaGGUGuau -5'
8666	3'	-48.8	NC_002229.2	+	3972	0.91	0.146963
	Target:  5'- gAUGUUGCCCCAGAAGUUUU-CACAUAg -3' miRNA:   3'- -UACAACGGGGUCUUCAAAAgGUGUAU- -5'
8666	3'	-48.8	NC_002229.2	+	134740	1.06	0.018975
	Target:  5'- gAUGUUGCCCCAGAAGUUUUCCACAUAg -3' miRNA:   3'- -UACAACGGGGUCUUCAAAAGGUGUAU- -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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