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
22335	3'	-57.5	NC_005045.1	+	14755	0.69	0.385975
	Target:  5'- -cGGCCCugcacaUCCUGCUgGGUGGCGg -3' miRNA:   3'- guUCGGGcuca--AGGGCGAgCCACUGC- -5'
22335	3'	-57.5	NC_005045.1	+	16519	0.7	0.296118
	Target:  5'- cCGAGCaccugaCCGAGcaaUCCCGCuUCGGUGAgGu -3' miRNA:   3'- -GUUCG------GGCUCa--AGGGCG-AGCCACUgC- -5'
22335	3'	-57.5	NC_005045.1	+	18998	1.09	0.000463
	Target:  5'- aCAAGCCCGAGUUCCCGCUCGGUGACGa -3' miRNA:   3'- -GUUCGGGCUCAAGGGCGAGCCACUGC- -5'
22335	3'	-57.5	NC_005045.1	+	28740	0.67	0.451809
	Target:  5'- uGAGCCUggaugGAGUgcgCCUGCUCGGcGAgGu -3' miRNA:   3'- gUUCGGG-----CUCAa--GGGCGAGCCaCUgC- -5'
22335	3'	-57.5	NC_005045.1	+	39095	0.7	0.311169
	Target:  5'- ----gCCGuGUcagcuucgCCCGCUCGGUGGCGg -3' miRNA:   3'- guucgGGCuCAa-------GGGCGAGCCACUGC- -5'
22335	3'	-57.5	NC_005045.1	+	39555	0.69	0.377099
	Target:  5'- uCAAGCCCGAGcuguaCCUGC-CGGcgcUGAUGg -3' miRNA:   3'- -GUUCGGGCUCaa---GGGCGaGCC---ACUGC- -5'
22335	3'	-57.5	NC_005045.1	+	40395	0.7	0.296118
	Target:  5'- -cGGCgaGGGUgccuuugCCCGcCUCGGUGGCGg -3' miRNA:   3'- guUCGggCUCAa------GGGC-GAGCCACUGC- -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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