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
16650	5'	-55.5	NC_004156.1	+	44433	0.66	0.957475
	Target:  5'- gGCCGUCagcUCUGugcacAGCaccucaaGCACCGGCAUc -3' miRNA:   3'- -UGGCAGc--AGACu----UCGa------UGUGGCCGUA- -5'
16650	5'	-55.5	NC_004156.1	+	123155	0.68	0.896829
	Target:  5'- cACCGcCaUCUGAAGCUACACaagccuccucugCGGCu- -3' miRNA:   3'- -UGGCaGcAGACUUCGAUGUG------------GCCGua -5'
16650	5'	-55.5	NC_004156.1	+	109430	0.69	0.876533
	Target:  5'- uGCCGa-GaCUGggGCUcuacucucgGCACCGGCAUc -3' miRNA:   3'- -UGGCagCaGACuuCGA---------UGUGGCCGUA- -5'
16650	5'	-55.5	NC_004156.1	+	127039	0.69	0.861933
	Target:  5'- -aCGUCGUCgcGAGCauCACCGGCAa -3' miRNA:   3'- ugGCAGCAGacUUCGauGUGGCCGUa -5'
16650	5'	-55.5	NC_004156.1	+	123116	0.73	0.66119
	Target:  5'- cACCGgccUCuUCUGAAcCUACACCGGCAUc -3' miRNA:   3'- -UGGC---AGcAGACUUcGAUGUGGCCGUA- -5'
16650	5'	-55.5	NC_004156.1	+	123236	0.82	0.245657
	Target:  5'- cACCGgCcUCUGAAGCUACACCGGCu- -3' miRNA:   3'- -UGGCaGcAGACUUCGAUGUGGCCGua -5'
16650	5'	-55.5	NC_004156.1	+	123191	1.05	0.008358
	Target:  5'- cACCGUCGUCUGAAGCUACACCGGCAUc -3' miRNA:   3'- -UGGCAGCAGACUUCGAUGUGGCCGUA- -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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