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
13452	5'	-55.5	NC_003409.1	+	35344	0.66	0.900145
	Target:  5'- uACCAUGgcagaagGCGGuuuuggAGCGGacucggUGgGGCGCg -3' miRNA:   3'- -UGGUAUa------CGCU------UCGCCa-----ACgCCGCGa -5'
13452	5'	-55.5	NC_003409.1	+	76782	0.66	0.879474
	Target:  5'- cACCAg----GAGGCGGUUuaGCGGUGCc -3' miRNA:   3'- -UGGUauacgCUUCGCCAA--CGCCGCGa -5'
13452	5'	-55.5	NC_003409.1	+	33878	0.67	0.864539
	Target:  5'- aGCCAUcauUGCguGAAGC--UUGUGGCGCUg -3' miRNA:   3'- -UGGUAu--ACG--CUUCGccAACGCCGCGA- -5'
13452	5'	-55.5	NC_003409.1	+	109846	0.67	0.848733
	Target:  5'- cGCCGcg-GCGGgaGGCGGUggcgccCGGCGCa -3' miRNA:   3'- -UGGUauaCGCU--UCGCCAac----GCCGCGa -5'
13452	5'	-55.5	NC_003409.1	+	87910	0.68	0.787379
	Target:  5'- aGCCGUGUuucGUGcuGCGGcuuggGCGGCGCc -3' miRNA:   3'- -UGGUAUA---CGCuuCGCCaa---CGCCGCGa -5'
13452	5'	-55.5	NC_003409.1	+	100073	0.74	0.445442
	Target:  5'- uGCCAUG-GCGggGCGGcUGUGGCa-- -3' miRNA:   3'- -UGGUAUaCGCuuCGCCaACGCCGcga -5'
13452	5'	-55.5	NC_003409.1	+	117139	1.08	0.002993
	Target:  5'- cACCAUAUGCGAAGCGGUUGCGGCGCUa -3' miRNA:   3'- -UGGUAUACGCUUCGCCAACGCCGCGA- -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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