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
26821	5'	-49.4	NC_005809.1	+	39620	0.67	0.865833
	Target:  5'- -cGAUCacgUGCUCGA--CGUGCCGCGc- -3' miRNA:   3'- uuUUAG---ACGAGCUacGCAUGGCGUuc -5'
26821	5'	-49.4	NC_005809.1	+	9700	0.67	0.856997
	Target:  5'- ----gCUGCUCaacGUGUACCGCGAc -3' miRNA:   3'- uuuuaGACGAGcuaCGCAUGGCGUUc -5'
26821	5'	-49.4	NC_005809.1	+	39891	0.7	0.732984
	Target:  5'- cGGcgCUGCUCGG-GCGUGCCGa--- -3' miRNA:   3'- uUUuaGACGAGCUaCGCAUGGCguuc -5'
26821	5'	-49.4	NC_005809.1	+	38064	0.7	0.686685
	Target:  5'- gAGGcgCUGCUCGGUGC--GCCagGCGAGg -3' miRNA:   3'- -UUUuaGACGAGCUACGcaUGG--CGUUC- -5'
26821	5'	-49.4	NC_005809.1	+	5692	0.71	0.663114
	Target:  5'- cAAAAUCUcGCUCGAUGacagACCGCcAGa -3' miRNA:   3'- -UUUUAGA-CGAGCUACgca-UGGCGuUC- -5'
26821	5'	-49.4	NC_005809.1	+	28063	0.71	0.627537
	Target:  5'- -cGGUCUGCUCGAacaGCGggcaggugGCCGCGGc -3' miRNA:   3'- uuUUAGACGAGCUa--CGCa-------UGGCGUUc -5'
26821	5'	-49.4	NC_005809.1	+	31932	0.76	0.356469
	Target:  5'- gGGGGUCuUGCacggCGAggGCGUGCCGCAGGa -3' miRNA:   3'- -UUUUAG-ACGa---GCUa-CGCAUGGCGUUC- -5'
26821	5'	-49.4	NC_005809.1	+	2736	0.98	0.014307
	Target:  5'- gAAAAUCUGCUCGAUGCG-ACCGCAAGa -3' miRNA:   3'- -UUUUAGACGAGCUACGCaUGGCGUUC- -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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