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
11299	5'	-53.3	NC_003083.1	+	51321	0.66	0.944763
	Target:  5'- aGCGCAAGCCGCguuguugGCGcaaacUGGCCGa--- -3' miRNA:   3'- cCGUGUUCGGUGa------UGC-----ACUGGCguac -5'
11299	5'	-53.3	NC_003083.1	+	35155	0.66	0.944763
	Target:  5'- uGGCGCAcGCUAUcaUugGUGAUgCGCGUc -3' miRNA:   3'- -CCGUGUuCGGUG--AugCACUG-GCGUAc -5'
11299	5'	-53.3	NC_003083.1	+	11820	0.67	0.906172
	Target:  5'- cGCGCAAGCCAaUACGaguuUGugCGUAc- -3' miRNA:   3'- cCGUGUUCGGUgAUGC----ACugGCGUac -5'
11299	5'	-53.3	NC_003083.1	+	62812	0.67	0.899638
	Target:  5'- cGCGCGuGGCgGCUgacaGCGUGACUaGCGUGc -3' miRNA:   3'- cCGUGU-UCGgUGA----UGCACUGG-CGUAC- -5'
11299	5'	-53.3	NC_003083.1	+	99562	0.67	0.899638
	Target:  5'- uGGCGCugcauuuGCCugUA-GUGAUCGUGUGu -3' miRNA:   3'- -CCGUGuu-----CGGugAUgCACUGGCGUAC- -5'
11299	5'	-53.3	NC_003083.1	+	115281	0.72	0.651658
	Target:  5'- uGGCGCcguuggcGGCCACuUGCGcUGugUGCAUGg -3' miRNA:   3'- -CCGUGu------UCGGUG-AUGC-ACugGCGUAC- -5'
11299	5'	-53.3	NC_003083.1	+	19910	1.12	0.002601
	Target:  5'- uGGCACAAGCCACUACGUGACCGCAUGg -3' miRNA:   3'- -CCGUGUUCGGUGAUGCACUGGCGUAC- -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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