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
30493	5'	-55.3	NC_006548.1	+	17192	0.66	0.56694
	Target:  5'- aCCUCGGCccGGCccgUUGGCUGAccgAGUg- -3' miRNA:   3'- -GGAGCCGc-CCGuu-GACCGACU---UCAau -5'
30493	5'	-55.3	NC_006548.1	+	27775	0.66	0.56694
	Target:  5'- aCCa-GGCGGGaauaGGCuUGGCUGguGUUGa -3' miRNA:   3'- -GGagCCGCCCg---UUG-ACCGACuuCAAU- -5'
30493	5'	-55.3	NC_006548.1	+	3630	0.67	0.533559
	Target:  5'- gCCUCGGCGcuCAGCgucauggucggGGCUGAAGc-- -3' miRNA:   3'- -GGAGCCGCccGUUGa----------CCGACUUCaau -5'
30493	5'	-55.3	NC_006548.1	+	778	0.68	0.47963
	Target:  5'- gUUCGGCGuGGCcaaggucGCaUGGCUGAAGa-- -3' miRNA:   3'- gGAGCCGC-CCGu------UG-ACCGACUUCaau -5'
30493	5'	-55.3	NC_006548.1	+	17664	0.69	0.39942
	Target:  5'- cCCUCGGCcauggccuGGGCGuauugaucaagACUGaGCUGggGa-- -3' miRNA:   3'- -GGAGCCG--------CCCGU-----------UGAC-CGACuuCaau -5'
30493	5'	-55.3	NC_006548.1	+	13367	0.71	0.328315
	Target:  5'- uCCUgCGGCGGGCAAaccGGCgccGAGGg-- -3' miRNA:   3'- -GGA-GCCGCCCGUUga-CCGa--CUUCaau -5'
30493	5'	-55.3	NC_006548.1	+	814	1.09	0.00056
	Target:  5'- aCCUCGGCGGGCAACUGGCUGAAGUUAu -3' miRNA:   3'- -GGAGCCGCCCGUUGACCGACUUCAAU- -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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