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
8823	3'	-55.7	NC_002484.1	+	41014	0.66	0.713539
	Target:  5'- --cGUGGGUgaaGGCCUCcgACUacGACGCc -3' miRNA:   3'- guaCGCCCA---UCGGAGa-UGGcuCUGCG- -5'
8823	3'	-55.7	NC_002484.1	+	25345	0.67	0.636552
	Target:  5'- uCAUGCGGGU-GCCUC-GCC-AGcgaaugggcuucaGCGCu -3' miRNA:   3'- -GUACGCCCAuCGGAGaUGGcUC-------------UGCG- -5'
8823	3'	-55.7	NC_002484.1	+	48826	0.69	0.508535
	Target:  5'- cCAUGCGGu--GCUUCUGCCGGcGgGCa -3' miRNA:   3'- -GUACGCCcauCGGAGAUGGCUcUgCG- -5'
8823	3'	-55.7	NC_002484.1	+	26453	0.7	0.477804
	Target:  5'- cCGUGCGcGGcucGGCUUcCUGCCGGccGGCGCa -3' miRNA:   3'- -GUACGC-CCa--UCGGA-GAUGGCU--CUGCG- -5'
8823	3'	-55.7	NC_002484.1	+	44480	0.71	0.400768
	Target:  5'- --cGUGGGcggcGCCgucagCUACCGAGACGg -3' miRNA:   3'- guaCGCCCau--CGGa----GAUGGCUCUGCg -5'
8823	3'	-55.7	NC_002484.1	+	31010	0.72	0.339395
	Target:  5'- cCAUGCuGGGggAGCCUCUcaaaaauGCCGcgugaucugcgGGGCGCa -3' miRNA:   3'- -GUACG-CCCa-UCGGAGA-------UGGC-----------UCUGCG- -5'
8823	3'	-55.7	NC_002484.1	+	17612	1.12	0.000598
	Target:  5'- gCAUGCGGGUAGCCUCUACCGAGACGCg -3' miRNA:   3'- -GUACGCCCAUCGGAGAUGGCUCUGCG- -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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