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
9808	3'	-55.9	NC_002593.1	+	35631	0.66	0.830807
	Target:  5'- gGUCGUCAUCAGaCAGGuGcuGCUGGUagucGCCu -3' miRNA:   3'- -CGGUAGUGGUU-GUCC-Cc-CGACCA----UGG- -5'
9808	3'	-55.9	NC_002593.1	+	35484	0.66	0.839295
	Target:  5'- cGUCGUCGCCAccggagGCgAGGGGuuGUUGGUGg- -3' miRNA:   3'- -CGGUAGUGGU------UG-UCCCC--CGACCAUgg -5'
9808	3'	-55.9	NC_002593.1	+	29446	0.66	0.834225
	Target:  5'- cGCCGUCACCGugcacgagcuuggccACAuuuuGGGGUUGGgucACa -3' miRNA:   3'- -CGGUAGUGGU---------------UGUc---CCCCGACCa--UGg -5'
9808	3'	-55.9	NC_002593.1	+	10270	0.67	0.766551
	Target:  5'- uGCCAUUAauagGACGGGGGGgUcGUACUa -3' miRNA:   3'- -CGGUAGUgg--UUGUCCCCCgAcCAUGG- -5'
9808	3'	-55.9	NC_002593.1	+	7849	0.72	0.509548
	Target:  5'- cGCCAUUaucacaagACCGAgAGGGGGCacGUACg -3' miRNA:   3'- -CGGUAG--------UGGUUgUCCCCCGacCAUGg -5'
9808	3'	-55.9	NC_002593.1	+	67450	0.72	0.519567
	Target:  5'- aCCAUCACCAcuaACGGccaGGGCUuGGUcACCg -3' miRNA:   3'- cGGUAGUGGU---UGUCc--CCCGA-CCA-UGG- -5'
9808	3'	-55.9	NC_002593.1	+	35312	1.13	0.000972
	Target:  5'- cGCCAUCACCAACAGGGGGCUGGUACCc -3' miRNA:   3'- -CGGUAGUGGUUGUCCCCCGACCAUGG- -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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