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
22282	5'	-58.6	NC_005045.1	+	31670	0.66	0.512365
	Target:  5'- aCCGcGUCGAguuGGcCCUGUACuuGGg -3' miRNA:   3'- gGGC-CAGCUaguCCaGGACGUGggCU- -5'
22282	5'	-58.6	NC_005045.1	+	4345	0.66	0.502107
	Target:  5'- uUCCGGUgagaUGuAUCGGGUagUGCAgCCCGAg -3' miRNA:   3'- -GGGCCA----GC-UAGUCCAggACGU-GGGCU- -5'
22282	5'	-58.6	NC_005045.1	+	24684	0.67	0.462032
	Target:  5'- --aGGcCGGUCAGGUCCaGUuucuccagcacGCCCGGc -3' miRNA:   3'- gggCCaGCUAGUCCAGGaCG-----------UGGGCU- -5'
22282	5'	-58.6	NC_005045.1	+	20127	0.67	0.452277
	Target:  5'- cCUCGGUCu-UCGGGUaggacuggaagaCCUGCAUgCCGAg -3' miRNA:   3'- -GGGCCAGcuAGUCCA------------GGACGUG-GGCU- -5'
22282	5'	-58.6	NC_005045.1	+	15054	0.71	0.257068
	Target:  5'- uCCCGG-CGGUgccgCAGGUCUaaUGCGCCUGc -3' miRNA:   3'- -GGGCCaGCUA----GUCCAGG--ACGUGGGCu -5'
22282	5'	-58.6	NC_005045.1	+	6592	0.73	0.173981
	Target:  5'- gCCGaaGUCaAUCAGGUCCUGCGCCa-- -3' miRNA:   3'- gGGC--CAGcUAGUCCAGGACGUGGgcu -5'
22282	5'	-58.6	NC_005045.1	+	34251	1.1	0.000363
	Target:  5'- uCCCGGUCGAUCAGGUCCUGCACCCGAu -3' miRNA:   3'- -GGGCCAGCUAGUCCAGGACGUGGGCU- -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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