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
21178	5'	-43.4	NC_004777.1	+	7406	0.69	0.979895
	Target:  5'- aCGCUggcaGCGCGGGUCuuuguuGGGAAUAGUCa- -3' miRNA:   3'- aGCGA----UGCGUUUAG------UCUUUAUUAGga -5'
21178	5'	-43.4	NC_004777.1	+	7923	0.74	0.872158
	Target:  5'- aCGCUGCGCGugguAUCAGAAA-GGUCg- -3' miRNA:   3'- aGCGAUGCGUu---UAGUCUUUaUUAGga -5'
21178	5'	-43.4	NC_004777.1	+	22817	0.69	0.982419
	Target:  5'- gUCGCUACGUGGAUUAGc---GGUCUUg -3' miRNA:   3'- -AGCGAUGCGUUUAGUCuuuaUUAGGA- -5'
21178	5'	-43.4	NC_004777.1	+	27574	0.66	0.998776
	Target:  5'- aCGCUugGCAGucaGUCGGucagcgucaaGAAUAA-CCUg -3' miRNA:   3'- aGCGAugCGUU---UAGUC----------UUUAUUaGGA- -5'
21178	5'	-43.4	NC_004777.1	+	28362	0.67	0.997144
	Target:  5'- cCGCUAaugcccuuggucUGCGAGUUAcAGAUGGUCCa -3' miRNA:   3'- aGCGAU------------GCGUUUAGUcUUUAUUAGGa -5'
21178	5'	-43.4	NC_004777.1	+	32894	0.7	0.963115
	Target:  5'- cUGCUGCGCAucAAUCuGAGGUAAacgcugagaacUCCg -3' miRNA:   3'- aGCGAUGCGU--UUAGuCUUUAUU-----------AGGa -5'
21178	5'	-43.4	NC_004777.1	+	34797	1.11	0.008344
	Target:  5'- gUCGCUACGCAAAUCAGAAAUAAUCCUa -3' miRNA:   3'- -AGCGAUGCGUUUAGUCUUUAUUAGGA- -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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