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
21157	3'	-51.4	NC_004775.1	+	14881	0.66	0.778146
	Target:  5'- cGGUGAACaucuuucGUGUGAUGUucccggaUGCCGACa -3' miRNA:   3'- -UUAUUUGgu-----CGCACUACG-------ACGGCUGa -5'
21157	3'	-51.4	NC_004775.1	+	38235	0.66	0.777071
	Target:  5'- --aGAACaGGCacaagaaauaauUGAUGCUGCCGACg -3' miRNA:   3'- uuaUUUGgUCGc-----------ACUACGACGGCUGa -5'
21157	3'	-51.4	NC_004775.1	+	4188	0.68	0.665559
	Target:  5'- --aGAAUCAGCGUGuuucccUGUUGCCuGGCg -3' miRNA:   3'- uuaUUUGGUCGCACu-----ACGACGG-CUGa -5'
21157	3'	-51.4	NC_004775.1	+	1993	0.68	0.653768
	Target:  5'- ----cGCCGGCaaggGUGAcgcgcUGCUGCUGACg -3' miRNA:   3'- uuauuUGGUCG----CACU-----ACGACGGCUGa -5'
21157	3'	-51.4	NC_004775.1	+	14846	0.69	0.594712
	Target:  5'- cAGUGAuCCAGCGUuuacagcaGAUGUUgcGCCGACg -3' miRNA:   3'- -UUAUUuGGUCGCA--------CUACGA--CGGCUGa -5'
21157	3'	-51.4	NC_004775.1	+	28710	0.72	0.427434
	Target:  5'- uGAUGGugCGGCGguUGAcUGCUGCCaGGCUg -3' miRNA:   3'- -UUAUUugGUCGC--ACU-ACGACGG-CUGA- -5'
21157	3'	-51.4	NC_004775.1	+	29301	1.05	0.002283
	Target:  5'- gAAUAAACCAGCGUGAUGCUGCCGACUc -3' miRNA:   3'- -UUAUUUGGUCGCACUACGACGGCUGA- -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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