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
24154	5'	-52	NC_005263.2	+	13007	0.65	0.87939
	Target:  5'- gCCGGUcgGCGUgaugccgaguagCUUGAUCAGCg-GGa -3' miRNA:   3'- aGGCCAa-CGCAa-----------GGACUAGUUGgaCC- -5'
24154	5'	-52	NC_005263.2	+	38665	0.66	0.873045
	Target:  5'- cCCGuGgUGCccgUCUUGAUCGGCCcGGg -3' miRNA:   3'- aGGC-CaACGca-AGGACUAGUUGGaCC- -5'
24154	5'	-52	NC_005263.2	+	24884	0.68	0.760307
	Target:  5'- gCCGG--GCGU--CUGcgCAACCUGGa -3' miRNA:   3'- aGGCCaaCGCAagGACuaGUUGGACC- -5'
24154	5'	-52	NC_005263.2	+	42438	0.69	0.695261
	Target:  5'- aCCGaGUUGCGcUUCCUGcgUAACgaacaaCUGGa -3' miRNA:   3'- aGGC-CAACGC-AAGGACuaGUUG------GACC- -5'
24154	5'	-52	NC_005263.2	+	39721	0.7	0.650447
	Target:  5'- gCCGGc-GCGggCCgcGUCGACCUGGc -3' miRNA:   3'- aGGCCaaCGCaaGGacUAGUUGGACC- -5'
24154	5'	-52	NC_005263.2	+	26249	0.7	0.648193
	Target:  5'- gCCGGccgucgcgaacGCGgcgaCCUGAUCAGCCUGa -3' miRNA:   3'- aGGCCaa---------CGCaa--GGACUAGUUGGACc -5'
24154	5'	-52	NC_005263.2	+	39709	0.72	0.506124
	Target:  5'- gCCGaGgcgGCGcgcUUCCUGGUCGGCCUGc -3' miRNA:   3'- aGGC-Caa-CGC---AAGGACUAGUUGGACc -5'
24154	5'	-52	NC_005263.2	+	32465	1.11	0.001482
	Target:  5'- aUCCGGUUGCGUUCCUGAUCAACCUGGc -3' miRNA:   3'- -AGGCCAACGCAAGGACUAGUUGGACC- -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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