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
31481	3'	-45.3	NC_006653.1	+	18295	0.67	0.941711
	Target:  5'- uUUUUUUcAUAUGCUcUUAUGGCaUCCGa -3' miRNA:   3'- -AAAAAA-UAUGCGGaAAUACCGaGGGC- -5'
31481	3'	-45.3	NC_006653.1	+	5697	0.69	0.847158
	Target:  5'- aUUUUUAuucUAUGCCUUUAUGGCaUuuGu -3' miRNA:   3'- aAAAAAU---AUGCGGAAAUACCGaGggC- -5'
31481	3'	-45.3	NC_006653.1	+	4164	0.71	0.782804
	Target:  5'- uUUUUUUcAUAUGCCcUUAUGGCaUCCGa -3' miRNA:   3'- -AAAAAA-UAUGCGGaAAUACCGaGGGC- -5'
31481	3'	-45.3	NC_006653.1	+	17733	0.84	0.186339
	Target:  5'- aUUUUUAuucUACGCCUUUAUGGCauacgaagugagUCCCGg -3' miRNA:   3'- aAAAAAU---AUGCGGAAAUACCG------------AGGGC- -5'
31481	3'	-45.3	NC_006653.1	+	3605	0.84	0.186339
	Target:  5'- aUUUUUAugaUACGCCUUUAUGGCauccgaagugggUCCCGg -3' miRNA:   3'- aAAAAAU---AUGCGGAAAUACCG------------AGGGC- -5'
31481	3'	-45.3	NC_006653.1	+	4075	1.09	0.004162
	Target:  5'- uUUUUUUAUACGCCUUUAUGGCUCCCGa -3' miRNA:   3'- -AAAAAAUAUGCGGAAAUACCGAGGGC- -5'
31481	3'	-45.3	NC_006653.1	+	18206	1.09	0.004162
	Target:  5'- uUUUUUUAUACGCCUUUAUGGCUCCCGa -3' miRNA:   3'- -AAAAAAUAUGCGGAAAUACCGAGGGC- -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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