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
2337	5'	-50	NC_001416.1	+	6951	1.12	0.002491
	Target:  5'- uCCACGUACUGUCCGGAAUACACGACGa -3' miRNA:   3'- -GGUGCAUGACAGGCCUUAUGUGCUGC- -5'
2337	5'	-50	NC_001416.1	+	2852	0.71	0.770795
	Target:  5'- cCCACccuuCUGgggCCGGAcgGCAUGACa -3' miRNA:   3'- -GGUGcau-GACa--GGCCUuaUGUGCUGc -5'
2337	5'	-50	NC_001416.1	+	4749	0.68	0.88865
	Target:  5'- cCCGCGUccgGCUGaccagcgugCCGGAcaccggcaGCACGGCGa -3' miRNA:   3'- -GGUGCA---UGACa--------GGCCUua------UGUGCUGC- -5'
2337	5'	-50	NC_001416.1	+	13249	0.68	0.903091
	Target:  5'- gCCACgGUACUGgagucguuUCUGGAAgaGCACGGgGg -3' miRNA:   3'- -GGUG-CAUGAC--------AGGCCUUa-UGUGCUgC- -5'
2337	5'	-50	NC_001416.1	+	19403	0.66	0.939535
	Target:  5'- uCCAuUGUACUG-CCGGAccAC-CGACu -3' miRNA:   3'- -GGU-GCAUGACaGGCCUuaUGuGCUGc -5'
2337	5'	-50	NC_001416.1	+	39676	0.66	0.949371
	Target:  5'- uUCGuCGUACUGuUCCGGcauguuGUugGCGAUc -3' miRNA:   3'- -GGU-GCAUGAC-AGGCCu-----UAugUGCUGc -5'
2337	5'	-50	NC_001416.1	+	27993	0.66	0.953865
	Target:  5'- aCCuuGaUACUGUgCCGGAugaaagcgGUuCGCGACGa -3' miRNA:   3'- -GGugC-AUGACA-GGCCU--------UAuGUGCUGC- -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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