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
20660	5'	-52.9	NC_004688.1	+	108114	0.66	0.960902
	Target:  5'- cUCUUUGCCgccaaggcccucaauCuUGAUGUCGUCggcgAUCAGg -3' miRNA:   3'- -AGAAGCGG---------------GcACUACAGCAGa---UGGUC- -5'
20660	5'	-52.9	NC_004688.1	+	1435	0.67	0.915561
	Target:  5'- --cUCGCCCGUGGg--CGUCgaucGCCGa -3' miRNA:   3'- agaAGCGGGCACUacaGCAGa---UGGUc -5'
20660	5'	-52.9	NC_004688.1	+	63762	0.67	0.915561
	Target:  5'- -gUUCGCCCuGgcgGGUGagGUCUACgAGa -3' miRNA:   3'- agAAGCGGG-Ca--CUACagCAGAUGgUC- -5'
20660	5'	-52.9	NC_004688.1	+	101056	0.69	0.859469
	Target:  5'- ---cCGCCCG-GAUGUCGcUCUuaucgagggaggGCCGGg -3' miRNA:   3'- agaaGCGGGCaCUACAGC-AGA------------UGGUC- -5'
20660	5'	-52.9	NC_004688.1	+	57311	0.7	0.79881
	Target:  5'- ---cUGCCCGcGGUGUCGaUgUACCAGg -3' miRNA:   3'- agaaGCGGGCaCUACAGC-AgAUGGUC- -5'
20660	5'	-52.9	NC_004688.1	+	66779	0.7	0.789423
	Target:  5'- ---cCGUCCGgguugagGAUGUCGUCgcGCCAGa -3' miRNA:   3'- agaaGCGGGCa------CUACAGCAGa-UGGUC- -5'
20660	5'	-52.9	NC_004688.1	+	57605	0.76	0.500727
	Target:  5'- aCUUCGCCCGUGAggcgcaggUGUCG-CUcGCCAc -3' miRNA:   3'- aGAAGCGGGCACU--------ACAGCaGA-UGGUc -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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