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
21198	5'	-52.4	NC_004778.3	+	32832	0.66	0.953896
	Target:  5'- ----aGUUUCGgaCGCGGCuGGCCUa -3' miRNA:   3'- aaaagUAAAGCaaGCGUCGcCCGGGc -5'
21198	5'	-52.4	NC_004778.3	+	96345	0.67	0.949643
	Target:  5'- -gUUCAUguaCGUguagcgCgGCAGCGGGCCg- -3' miRNA:   3'- aaAAGUAaa-GCAa-----G-CGUCGCCCGGgc -5'
21198	5'	-52.4	NC_004778.3	+	118774	0.67	0.945138
	Target:  5'- ---aCGcUUCGggCGCGGCGcGGCCgGc -3' miRNA:   3'- aaaaGUaAAGCaaGCGUCGC-CCGGgC- -5'
21198	5'	-52.4	NC_004778.3	+	46691	0.67	0.930073
	Target:  5'- -cUUCGgcgUCGgaauUCGCGGCGGGgggaCCGu -3' miRNA:   3'- aaAAGUaa-AGCa---AGCGUCGCCCg---GGC- -5'
21198	5'	-52.4	NC_004778.3	+	107142	0.68	0.899756
	Target:  5'- ---cCAUgUCGUUgGUGGCGGGCgCGc -3' miRNA:   3'- aaaaGUAaAGCAAgCGUCGCCCGgGC- -5'
21198	5'	-52.4	NC_004778.3	+	91299	0.7	0.846849
	Target:  5'- --gUCGag-CGg-CGCAGCGGGCCUGc -3' miRNA:   3'- aaaAGUaaaGCaaGCGUCGCCCGGGC- -5'
21198	5'	-52.4	NC_004778.3	+	14753	0.7	0.838383
	Target:  5'- -------cUCGUUauauaGCAGCGGGCCUa -3' miRNA:   3'- aaaaguaaAGCAAg----CGUCGCCCGGGc -5'
21198	5'	-52.4	NC_004778.3	+	106555	1.07	0.006811
	Target:  5'- aUUUUCAUUUCGUUCGCAGCGGGCCCGu -3' miRNA:   3'- -AAAAGUAAAGCAAGCGUCGCCCGGGC- -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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