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
779	3'	-55.2	NC_000852.3	+	211551	0.67	0.982368
	Target:  5'- uGGCcggaggacuUUCACaGCUCgUCGCGUacggUGCCCa -3' miRNA:   3'- gUCG---------AAGUGcUGAG-AGCGCAg---ACGGG- -5'
779	3'	-55.2	NC_000852.3	+	61769	0.68	0.968057
	Target:  5'- ---aUUCACGGacaCUCGuCGUCUGUCCa -3' miRNA:   3'- gucgAAGUGCUga-GAGC-GCAGACGGG- -5'
779	3'	-55.2	NC_000852.3	+	156389	0.68	0.965043
	Target:  5'- uCAGCUUCG-GGCuUCUCGCGguaUGCgCu -3' miRNA:   3'- -GUCGAAGUgCUG-AGAGCGCag-ACGgG- -5'
779	3'	-55.2	NC_000852.3	+	97585	0.68	0.954819
	Target:  5'- -cGUUUUGCGACUUUCaaGUCUGCUUu -3' miRNA:   3'- guCGAAGUGCUGAGAGcgCAGACGGG- -5'
779	3'	-55.2	NC_000852.3	+	109088	0.68	0.954446
	Target:  5'- gCAGCUcCAUGAC-CUauaaacguuccccCGUGUUUGCCCc -3' miRNA:   3'- -GUCGAaGUGCUGaGA-------------GCGCAGACGGG- -5'
779	3'	-55.2	NC_000852.3	+	40991	0.69	0.942739
	Target:  5'- gGGUUUCuACGGUUCggCGCGUgaGCCCa -3' miRNA:   3'- gUCGAAG-UGCUGAGa-GCGCAgaCGGG- -5'
779	3'	-55.2	NC_000852.3	+	172823	0.69	0.933618
	Target:  5'- uGGCUUCGCGACUUgguUCGC-UUUGCa- -3' miRNA:   3'- gUCGAAGUGCUGAG---AGCGcAGACGgg -5'
779	3'	-55.2	NC_000852.3	+	178996	1.11	0.005896
	Target:  5'- uCAGCUUCACGACUCUCGCGUCUGCCCu -3' miRNA:   3'- -GUCGAAGUGCUGAGAGCGCAGACGGG- -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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