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
9729	5'	-53.6	NC_002577.1	+	81270	0.66	0.961419
	Target:  5'- --uGAgGUGGCCgcggGCGUGGCGCa--- -3' miRNA:   3'- cagUUgUACCGGg---CGCAUCGCGaaac -5'
9729	5'	-53.6	NC_002577.1	+	20268	0.66	0.95773
	Target:  5'- gGUCAcucgagACAUGGCCa-CGUAGaCGCUg-- -3' miRNA:   3'- -CAGU------UGUACCGGgcGCAUC-GCGAaac -5'
9729	5'	-53.6	NC_002577.1	+	160398	0.67	0.935696
	Target:  5'- gGUCGuaACAaGGCuCCGCGgAGCGCg--- -3' miRNA:   3'- -CAGU--UGUaCCG-GGCGCaUCGCGaaac -5'
9729	5'	-53.6	NC_002577.1	+	136939	0.67	0.935696
	Target:  5'- gGUCGuaACAaGGCuCCGCGgAGCGCg--- -3' miRNA:   3'- -CAGU--UGUaCCG-GGCGCaUCGCGaaac -5'
9729	5'	-53.6	NC_002577.1	+	70915	0.68	0.894449
	Target:  5'- -------cGGCCCGCGUcuuGGCGCUg-- -3' miRNA:   3'- caguuguaCCGGGCGCA---UCGCGAaac -5'
9729	5'	-53.6	NC_002577.1	+	112278	0.7	0.833173
	Target:  5'- -gCAGCAUGGCCCGUGacuCGCUc-- -3' miRNA:   3'- caGUUGUACCGGGCGCaucGCGAaac -5'
9729	5'	-53.6	NC_002577.1	+	66370	0.74	0.616189
	Target:  5'- uGUCugcguAUAUGGCCCGCGUGGCa----- -3' miRNA:   3'- -CAGu----UGUACCGGGCGCAUCGcgaaac -5'
9729	5'	-53.6	NC_002577.1	+	73094	1.1	0.004169
	Target:  5'- cGUCAACAUGGCCCGCGUAGCGCUUUGg -3' miRNA:   3'- -CAGUUGUACCGGGCGCAUCGCGAAAC- -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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