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
13450	5'	-57.5	NC_003409.1	+	112012	0.66	0.820113
	Target:  5'- -aCGGCCGccccCGCGGUGGccgaCGCGAGg -3' miRNA:   3'- gaGUUGGCca--GCGUCACCug--GCGCUC- -5'
13450	5'	-57.5	NC_003409.1	+	113074	0.67	0.808062
	Target:  5'- gUCu-UCGGUCGCAGccacaccgcgacgGGugUGCGAGg -3' miRNA:   3'- gAGuuGGCCAGCGUCa------------CCugGCGCUC- -5'
13450	5'	-57.5	NC_003409.1	+	94179	0.67	0.775722
	Target:  5'- -cCAGCCGGUUGUc--GGGCUGCGGa -3' miRNA:   3'- gaGUUGGCCAGCGucaCCUGGCGCUc -5'
13450	5'	-57.5	NC_003409.1	+	68225	0.69	0.668575
	Target:  5'- --aAACCGGUaGCAGUGGuagcggGCCGCGuGc -3' miRNA:   3'- gagUUGGCCAgCGUCACC------UGGCGCuC- -5'
13450	5'	-57.5	NC_003409.1	+	51491	0.7	0.622059
	Target:  5'- uUCAGCCGGUCGCcagggucaucccgccGGUugguGGugUGUGGGa -3' miRNA:   3'- gAGUUGGCCAGCG---------------UCA----CCugGCGCUC- -5'
13450	5'	-57.5	NC_003409.1	+	113248	0.73	0.480355
	Target:  5'- cCUCGcacACCcGUCGCGGUGuGGCUGCGAc -3' miRNA:   3'- -GAGU---UGGcCAGCGUCAC-CUGGCGCUc -5'
13450	5'	-57.5	NC_003409.1	+	116359	1.09	0.002076
	Target:  5'- cCUCAACCGGUCGCAGUGGACCGCGAGa -3' miRNA:   3'- -GAGUUGGCCAGCGUCACCUGGCGCUC- -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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