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
32103	5'	-58.2	NC_007016.1	+	10875	0.66	0.790964
	Target:  5'- gGcGUCGACgGGCCCGgcguggacuuugcaGUGGUGGUc- -3' miRNA:   3'- aC-CAGUUG-CCGGGCag------------CGCCACCAau -5'
32103	5'	-58.2	NC_007016.1	+	74400	0.66	0.76218
	Target:  5'- ---gCGGCGGguuaaCCGUCGCGGgGGUUGg -3' miRNA:   3'- accaGUUGCCg----GGCAGCGCCaCCAAU- -5'
32103	5'	-58.2	NC_007016.1	+	40324	0.67	0.756474
	Target:  5'- gUGGUCcugccagccugugccAACGGCCaCGUCuGCGGcaUGGg-- -3' miRNA:   3'- -ACCAG---------------UUGCCGG-GCAG-CGCC--ACCaau -5'
32103	5'	-58.2	NC_007016.1	+	46274	0.68	0.650975
	Target:  5'- aUGGUCucaacCGGCgauCCGUCGCGGgucaaugcgacgGGUUGu -3' miRNA:   3'- -ACCAGuu---GCCG---GGCAGCGCCa-----------CCAAU- -5'
32103	5'	-58.2	NC_007016.1	+	118687	0.69	0.59186
	Target:  5'- -cGUCAAaaaaGCCCGUCGCcGGUGGg-- -3' miRNA:   3'- acCAGUUgc--CGGGCAGCG-CCACCaau -5'
32103	5'	-58.2	NC_007016.1	+	119053	0.75	0.287756
	Target:  5'- gGGUCcuggccgaGACGGCCCGgCGgGGUGGUc- -3' miRNA:   3'- aCCAG--------UUGCCGGGCaGCgCCACCAau -5'
32103	5'	-58.2	NC_007016.1	+	62706	1.06	0.002297
	Target:  5'- gUGGUCAACGGCCCGUCGCGGUGGUUAc -3' miRNA:   3'- -ACCAGUUGCCGGGCAGCGCCACCAAU- -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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