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
13052	3'	-61.1	NC_003390.1	+	47467	0.66	0.351286
	Target:  5'- -gCCACUaccugugaucaGGCcuugGCCUGCCAuGAGGGCAGc -3' miRNA:   3'- gaGGUGG-----------CCG----UGGGCGGU-CUUCCGUU- -5'
13052	3'	-61.1	NC_003390.1	+	24603	0.67	0.304027
	Target:  5'- -gUCACUGGCAUCC-CCaAGAGGGCc- -3' miRNA:   3'- gaGGUGGCCGUGGGcGG-UCUUCCGuu -5'
13052	3'	-61.1	NC_003390.1	+	10269	0.68	0.254606
	Target:  5'- aUCCGCCuGCAUCaCGCCgAGAucuacaaGGGCAAg -3' miRNA:   3'- gAGGUGGcCGUGG-GCGG-UCU-------UCCGUU- -5'
13052	3'	-61.1	NC_003390.1	+	14547	0.69	0.207575
	Target:  5'- gUCCGCgCGGCACagGCUcuuGAAGGCAAg -3' miRNA:   3'- gAGGUG-GCCGUGggCGGu--CUUCCGUU- -5'
13052	3'	-61.1	NC_003390.1	+	33969	0.7	0.191778
	Target:  5'- gCUCCauGCCGGauugUACCUGCgAGAGGGUAGa -3' miRNA:   3'- -GAGG--UGGCC----GUGGGCGgUCUUCCGUU- -5'
13052	3'	-61.1	NC_003390.1	+	40378	0.73	0.110906
	Target:  5'- -aCCACCGGUugCCGuCCAGGcgaauguGGGCGu -3' miRNA:   3'- gaGGUGGCCGugGGC-GGUCU-------UCCGUu -5'
13052	3'	-61.1	NC_003390.1	+	2423	1.06	0.000329
	Target:  5'- aCUCCACCGGCACCCGCCAGAAGGCAAc -3' miRNA:   3'- -GAGGUGGCCGUGGGCGGUCUUCCGUU- -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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