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
3228	3'	-58.2	NC_001514.1	+	2727	0.7	0.067105
	Target:  5'- aGUUCaUCCcgguagUGG-GGCCCUGGGGCu -3' miRNA:   3'- cCAGG-AGGua----ACCaCCGGGACUCCGu -5'
3228	3'	-58.2	NC_001514.1	+	6295	0.7	0.064942
	Target:  5'- aGGagCUCCucagGGcgagccuuuUGGCCCUGGGGCu -3' miRNA:   3'- -CCagGAGGuaa-CC---------ACCGGGACUCCGu -5'
3228	3'	-58.2	NC_001514.1	+	115	0.93	0.000641
	Target:  5'- aGGUCCUCCAUUGGUGGCCCgccaccacgcccGGGGCAu -3' miRNA:   3'- -CCAGGAGGUAACCACCGGGa-----------CUCCGU- -5'
3228	3'	-58.2	NC_001514.1	+	8436	0.93	0.000641
	Target:  5'- aGGUCCUCCAUUGGUGGCCCgccaccacgcccGGGGCAu -3' miRNA:   3'- -CCAGGAGGUAACCACCGGGa-----------CUCCGU- -5'
3228	3'	-58.2	NC_001514.1	+	201	1.02	0.000127
	Target:  5'- aGGUCCUUUAUUGGUGGCCCUGAGGCAu -3' miRNA:   3'- -CCAGGAGGUAACCACCGGGACUCCGU- -5'
3228	3'	-58.2	NC_001514.1	+	8522	1.02	0.000127
	Target:  5'- aGGUCCUUUAUUGGUGGCCCUGAGGCAu -3' miRNA:   3'- -CCAGGAGGUAACCACCGGGACUCCGU- -5'
3228	3'	-58.2	NC_001514.1	+	158	1.1	0.000023
	Target:  5'- aGGUCCUCCAUUGGUGGCCCUGAGGCAu -3' miRNA:   3'- -CCAGGAGGUAACCACCGGGACUCCGU- -5'
3228	3'	-58.2	NC_001514.1	+	8479	1.1	0.000023
	Target:  5'- aGGUCCUCCAUUGGUGGCCCUGAGGCAu -3' miRNA:   3'- -CCAGGAGGUAACCACCGGGACUCCGU- -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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