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
21857	3'	-51.4	NC_004902.1	+	39649	0.66	0.803018
	Target:  5'- -aGGg--UUGCUGCGCUggaagUUGUcacGGCa -3' miRNA:   3'- aaCCaaaGACGACGCGGa----AACAu--CCG- -5'
21857	3'	-51.4	NC_004902.1	+	18771	0.67	0.771474
	Target:  5'- cUGGUaua-GCUGCGCCUgUGcauccUGGGCc -3' miRNA:   3'- aACCAaagaCGACGCGGAaAC-----AUCCG- -5'
21857	3'	-51.4	NC_004902.1	+	35756	0.68	0.715806
	Target:  5'- -aGGaugagCUGCUGCGCCgccugauggcUGUggAGGCa -3' miRNA:   3'- aaCCaaa--GACGACGCGGaa--------ACA--UCCG- -5'
21857	3'	-51.4	NC_004902.1	+	11019	0.68	0.704335
	Target:  5'- -cGGUUUCcGCUGCuGCCaUUGcuGGCc -3' miRNA:   3'- aaCCAAAGaCGACG-CGGaAACauCCG- -5'
21857	3'	-51.4	NC_004902.1	+	30664	0.74	0.373193
	Target:  5'- -aGGUccuugcCUGCUGCGCCcUUGUcaaccAGGCa -3' miRNA:   3'- aaCCAaa----GACGACGCGGaAACA-----UCCG- -5'
21857	3'	-51.4	NC_004902.1	+	21380	0.78	0.212385
	Target:  5'- -cGGUgucugcugUCUGCUGCGCCgccUGUAGuGCc -3' miRNA:   3'- aaCCAa-------AGACGACGCGGaa-ACAUC-CG- -5'
21857	3'	-51.4	NC_004902.1	+	11127	1.11	0.001042
	Target:  5'- gUUGGUUUCUGCUGCGCCUUUGUAGGCg -3' miRNA:   3'- -AACCAAAGACGACGCGGAAACAUCCG- -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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