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
23361	5'	-57.5	NC_005259.1	+	25847	0.66	0.61547
	Target:  5'- cCUCGCGGauguGGUACucgAUgUGCGGGCgugugccAGCGa -3' miRNA:   3'- -GAGCGCC----CUAUG---UAgACGCCCG-------UCGU- -5'
23361	5'	-57.5	NC_005259.1	+	61411	0.66	0.605801
	Target:  5'- cCUCGCGGGcacggACAacacccUUGCGGGCGcGCc -3' miRNA:   3'- -GAGCGCCCua---UGUa-----GACGCCCGU-CGu -5'
23361	5'	-57.5	NC_005259.1	+	32480	0.67	0.574798
	Target:  5'- aCUCGcCGGGcgcgaggugguucuGUAUgaacaccgugagguaGUCgagGCGGGCGGCAg -3' miRNA:   3'- -GAGC-GCCC--------------UAUG---------------UAGa--CGCCCGUCGU- -5'
23361	5'	-57.5	NC_005259.1	+	41634	0.68	0.511021
	Target:  5'- aUgGUGGcGGUGCcgGUCUGCGGGC-GCu -3' miRNA:   3'- gAgCGCC-CUAUG--UAGACGCCCGuCGu -5'
23361	5'	-57.5	NC_005259.1	+	20974	0.68	0.497792
	Target:  5'- aUCGcCGGGGUgACAaCUGCgugugggccuacucGGGCGGCGa -3' miRNA:   3'- gAGC-GCCCUA-UGUaGACG--------------CCCGUCGU- -5'
23361	5'	-57.5	NC_005259.1	+	10170	0.69	0.48073
	Target:  5'- aUCuCGGGAaAC-UCUGaGGGCAGCAc -3' miRNA:   3'- gAGcGCCCUaUGuAGACgCCCGUCGU- -5'
23361	5'	-57.5	NC_005259.1	+	36544	0.69	0.451339
	Target:  5'- -aCGCGGGGUG-AUCUGCGGuGUGGgAu -3' miRNA:   3'- gaGCGCCCUAUgUAGACGCC-CGUCgU- -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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