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
31939	3'	-54.1	NC_006940.1	+	12618	0.66	0.669389
	Target:  5'- ---aCGCCUGgguuaucGCCGCAGCuaacgACCa -3' miRNA:   3'- gaagGCGGACaa-----CGGUGUCGua---UGGc -5'
31939	3'	-54.1	NC_006940.1	+	6465	0.68	0.522562
	Target:  5'- --aCCGCg-GUaGCCACGGCA-GCCGg -3' miRNA:   3'- gaaGGCGgaCAaCGGUGUCGUaUGGC- -5'
31939	3'	-54.1	NC_006940.1	+	38324	0.71	0.399153
	Target:  5'- -gUUCGCCUGgucUGCCAUAGCGc-CCGc -3' miRNA:   3'- gaAGGCGGACa--ACGGUGUCGUauGGC- -5'
31939	3'	-54.1	NC_006940.1	+	19081	0.71	0.362331
	Target:  5'- --gCCGCUUGUaccGCCACGGUAagcucUACCGg -3' miRNA:   3'- gaaGGCGGACAa--CGGUGUCGU-----AUGGC- -5'
31939	3'	-54.1	NC_006940.1	+	35625	0.74	0.25343
	Target:  5'- uCUUCCGgugucaucagaaucCCUGUUGCCcguugguuaagcauCGGCGUACCGg -3' miRNA:   3'- -GAAGGC--------------GGACAACGGu-------------GUCGUAUGGC- -5'
31939	3'	-54.1	NC_006940.1	+	15317	0.76	0.192339
	Target:  5'- gCUUCCGCCUGUUG-UGCAGUGUACg- -3' miRNA:   3'- -GAAGGCGGACAACgGUGUCGUAUGgc -5'
31939	3'	-54.1	NC_006940.1	+	14371	1.09	0.000878
	Target:  5'- gCUUCCGCCUGUUGCCACAGCAUACCGu -3' miRNA:   3'- -GAAGGCGGACAACGGUGUCGUAUGGC- -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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