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
29482	3'	-49.4	NC_006151.1	+	116105	0.66	0.994345
	Target:  5'- cGUCGgcGA-UGGCGCggcgcuugUCGGGCAGCAc -3' miRNA:   3'- uCAGUauUUcACCGUG--------AGUCUGUCGU- -5'
29482	3'	-49.4	NC_006151.1	+	84418	0.66	0.994345
	Target:  5'- cGGUgAUAAGGcGGCGCgc-GGCGGCGc -3' miRNA:   3'- -UCAgUAUUUCaCCGUGaguCUGUCGU- -5'
29482	3'	-49.4	NC_006151.1	+	103814	0.67	0.990442
	Target:  5'- uGUCGgcgGccGUGGCggcggccguggagauGCUCGGGCGGCu -3' miRNA:   3'- uCAGUa--UuuCACCG---------------UGAGUCUGUCGu -5'
29482	3'	-49.4	NC_006151.1	+	76067	0.67	0.989902
	Target:  5'- gAG-CGUGAAG-GGCGC-CAG-CAGCGa -3' miRNA:   3'- -UCaGUAUUUCaCCGUGaGUCuGUCGU- -5'
29482	3'	-49.4	NC_006151.1	+	139503	0.68	0.980959
	Target:  5'- cGGUCAUGGAGgacagcGGCAacagCAGcgGCAGCGa -3' miRNA:   3'- -UCAGUAUUUCa-----CCGUga--GUC--UGUCGU- -5'
29482	3'	-49.4	NC_006151.1	+	99243	0.69	0.970323
	Target:  5'- aGGUCGUGGA--GGCGCUCGuGACcGCGg -3' miRNA:   3'- -UCAGUAUUUcaCCGUGAGU-CUGuCGU- -5'
29482	3'	-49.4	NC_006151.1	+	47377	1.09	0.009483
	Target:  5'- aAGUCAUAAAGUGGCACUCAGACAGCAc -3' miRNA:   3'- -UCAGUAUUUCACCGUGAGUCUGUCGU- -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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