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
17482	3'	-56.6	NC_004456.1	+	32186	0.66	0.535505
	Target:  5'- cCUGacuacGCCGCCAGgcagcaaccugcUGGCCGGUGgCUUCa -3' miRNA:   3'- -GACcu---UGGCGGUC------------ACUGGCCGU-GAAG- -5'
17482	3'	-56.6	NC_004456.1	+	19874	0.67	0.514053
	Target:  5'- aCUGGccuguguUUGCCAG-GGCCuGCACUUCu -3' miRNA:   3'- -GACCuu-----GGCGGUCaCUGGcCGUGAAG- -5'
17482	3'	-56.6	NC_004456.1	+	21310	0.67	0.492961
	Target:  5'- -----cCCGCCAGUGAgCGGguUUUCu -3' miRNA:   3'- gaccuuGGCGGUCACUgGCCguGAAG- -5'
17482	3'	-56.6	NC_004456.1	+	42258	0.69	0.376184
	Target:  5'- uUGGuauGCCGUCAGUGACUuccuGGCgaGCUUUu -3' miRNA:   3'- gACCu--UGGCGGUCACUGG----CCG--UGAAG- -5'
17482	3'	-56.6	NC_004456.1	+	21085	0.71	0.291952
	Target:  5'- gUGGugaacGCUGCCGGUGACCugauuguuccaggcGGCACUg- -3' miRNA:   3'- gACCu----UGGCGGUCACUGG--------------CCGUGAag -5'
17482	3'	-56.6	NC_004456.1	+	17165	0.71	0.272461
	Target:  5'- uUGGaAACCGCUguaUGACCGGCGCg-- -3' miRNA:   3'- gACC-UUGGCGGuc-ACUGGCCGUGaag -5'
17482	3'	-56.6	NC_004456.1	+	24589	1.1	0.000453
	Target:  5'- aCUGGAACCGCCAGUGACCGGCACUUCu -3' miRNA:   3'- -GACCUUGGCGGUCACUGGCCGUGAAG- -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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