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
2336	3'	-51.5	NC_001416.1	+	9415	0.67	0.764425
	Target:  5'- --cGGUaaCAGCGGCAACCgGCAuGAccGUGa -3' miRNA:   3'- agaCCA--GUCGUCGUUGG-CGUuCU--UAC- -5'
2336	3'	-51.5	NC_001416.1	+	9310	0.68	0.720517
	Target:  5'- gCUgGGUCAGCAGUAuCgGUAAGGcgGu -3' miRNA:   3'- aGA-CCAGUCGUCGUuGgCGUUCUuaC- -5'
2336	3'	-51.5	NC_001416.1	+	37226	0.69	0.686523
	Target:  5'- uUCUGGUCGGC-GCAuaGCUgauaacaauugaGCAAGAAUc -3' miRNA:   3'- -AGACCAGUCGuCGU--UGG------------CGUUCUUAc -5'
2336	3'	-51.5	NC_001416.1	+	19335	0.7	0.628877
	Target:  5'- -gUGGUcCGGCAGUAcaauggauuACCGUAAGAcgGa -3' miRNA:   3'- agACCA-GUCGUCGU---------UGGCGUUCUuaC- -5'
2336	3'	-51.5	NC_001416.1	+	8495	0.73	0.420336
	Target:  5'- -gUGGUCAGCGGC-ACCGCcaucGGGAUu -3' miRNA:   3'- agACCAGUCGUCGuUGGCGu---UCUUAc -5'
2336	3'	-51.5	NC_001416.1	+	4683	0.76	0.323421
	Target:  5'- gCUGGUCAGCcggacgcgggcgcuGCAGCCGUAcucgGGGAUGa -3' miRNA:   3'- aGACCAGUCGu-------------CGUUGGCGU----UCUUAC- -5'
2336	3'	-51.5	NC_001416.1	+	5994	1.09	0.001836
	Target:  5'- gUCUGGUCAGCAGCAACCGCAAGAAUGc -3' miRNA:   3'- -AGACCAGUCGUCGUUGGCGUUCUUAC- -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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