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
12199	3'	-54.7	NC_003309.1	+	40593	0.67	0.710386
	Target:  5'- cGCaaggGAGCaACCGGUCGgCUCuacGGUguagCCg -3' miRNA:   3'- -CGa---CUCGcUGGUCAGC-GAGu--CCAa---GG- -5'
12199	3'	-54.7	NC_003309.1	+	15499	0.68	0.655871
	Target:  5'- uGCUGcGGCGGCauuucuUCGUUCGGG-UCCg -3' miRNA:   3'- -CGAC-UCGCUGguc---AGCGAGUCCaAGG- -5'
12199	3'	-54.7	NC_003309.1	+	31422	0.69	0.588726
	Target:  5'- cGCUG-GCGACCAGU-GCgCAGccgccggcgugccGUUCCu -3' miRNA:   3'- -CGACuCGCUGGUCAgCGaGUC-------------CAAGG- -5'
12199	3'	-54.7	NC_003309.1	+	4428	0.7	0.514463
	Target:  5'- ---cAGCGACUGGUCGCUCAGcGgcUCa -3' miRNA:   3'- cgacUCGCUGGUCAGCGAGUC-CaaGG- -5'
12199	3'	-54.7	NC_003309.1	+	39929	0.7	0.493617
	Target:  5'- aGUUGcaAGCGAUCuGaUCGCUCAGGgcaCCg -3' miRNA:   3'- -CGAC--UCGCUGGuC-AGCGAGUCCaa-GG- -5'
12199	3'	-54.7	NC_003309.1	+	37467	0.71	0.463101
	Target:  5'- aGCUGGcaagucCGACgAGUCGUUCAcGUUCCa -3' miRNA:   3'- -CGACUc-----GCUGgUCAGCGAGUcCAAGG- -5'
12199	3'	-54.7	NC_003309.1	+	41274	0.71	0.443316
	Target:  5'- cGCUG-GCGGCCGG--GCUCAGGUc-- -3' miRNA:   3'- -CGACuCGCUGGUCagCGAGUCCAagg -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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