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
30412	5'	-49.5	NC_006548.1	+	371	0.66	0.896479
	Target:  5'- -uGGGCCGGCAUcacguuuguuuuUCCGGUcaagGAUgAGc -3' miRNA:   3'- guUCCGGCCGUA------------AGGUUAa---CUAgUCu -5'
30412	5'	-49.5	NC_006548.1	+	8462	0.66	0.88069
	Target:  5'- uCGAGGCCGGCcuggCCGA--GcgUAGAg -3' miRNA:   3'- -GUUCCGGCCGuaa-GGUUaaCuaGUCU- -5'
30412	5'	-49.5	NC_006548.1	+	36649	0.67	0.863709
	Target:  5'- uGAGGCCGGCgcgcugaucugGUUCUacgagGAUUGGgcaaCAGAg -3' miRNA:   3'- gUUCCGGCCG-----------UAAGG-----UUAACUa---GUCU- -5'
30412	5'	-49.5	NC_006548.1	+	24430	0.7	0.671742
	Target:  5'- uCAAGGCCGGCAcguUUCCGGcc---CAGAc -3' miRNA:   3'- -GUUCCGGCCGU---AAGGUUaacuaGUCU- -5'
30412	5'	-49.5	NC_006548.1	+	402	0.7	0.659905
	Target:  5'- aGAGGaaCUGGUGUUCCAAUUGcAUCGGc -3' miRNA:   3'- gUUCC--GGCCGUAAGGUUAAC-UAGUCu -5'
30412	5'	-49.5	NC_006548.1	+	24010	0.74	0.452744
	Target:  5'- -cAGGCCgGGCGgugUCCAGccGAUCAGGg -3' miRNA:   3'- guUCCGG-CCGUa--AGGUUaaCUAGUCU- -5'
30412	5'	-49.5	NC_006548.1	+	4284	1.09	0.002176
	Target:  5'- gCAAGGCCGGCAUUCCAAUUGAUCAGAc -3' miRNA:   3'- -GUUCCGGCCGUAAGGUUAACUAGUCU- -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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