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
8797	5'	-52.8	NC_002484.1	+	39375	0.66	0.7946
	Target:  5'- cGGCGCUGGUGucaCGUUUgcaaugGCCGUGGc -3' miRNA:   3'- -UCGCGGUCGUuacGCAAAa-----CGGCACU- -5'
8797	5'	-52.8	NC_002484.1	+	31135	0.67	0.781426
	Target:  5'- -uCGUCGGCAAUGUGUUcUGCuaccgcgccacugaCGUGAa -3' miRNA:   3'- ucGCGGUCGUUACGCAAaACG--------------GCACU- -5'
8797	5'	-52.8	NC_002484.1	+	51837	0.67	0.774216
	Target:  5'- cGCGCCGGCuugGCGUgcUUGuCCuUGAu -3' miRNA:   3'- uCGCGGUCGuuaCGCAa-AAC-GGcACU- -5'
8797	5'	-52.8	NC_002484.1	+	8204	0.69	0.664947
	Target:  5'- cAGCGCUGGCGAUGUacucaggcaGUgggUUGCgCGUGu -3' miRNA:   3'- -UCGCGGUCGUUACG---------CAa--AACG-GCACu -5'
8797	5'	-52.8	NC_002484.1	+	32275	0.7	0.585745
	Target:  5'- cGGCGCCAuucaauGCAcggauUGCGgc--GCCGUGAa -3' miRNA:   3'- -UCGCGGU------CGUu----ACGCaaaaCGGCACU- -5'
8797	5'	-52.8	NC_002484.1	+	14468	0.7	0.563337
	Target:  5'- uAGCGCCAGCGAUGaauGUcaguaGCCGUc- -3' miRNA:   3'- -UCGCGGUCGUUACg--CAaaa--CGGCAcu -5'
8797	5'	-52.8	NC_002484.1	+	3834	1.09	0.001493
	Target:  5'- gAGCGCCAGCAAUGCGUUUUGCCGUGAc -3' miRNA:   3'- -UCGCGGUCGUUACGCAAAACGGCACU- -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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