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
21876	5'	-56.8	NC_004902.1	+	24414	0.67	0.479862
	Target:  5'- gUGAGCGcugucgGCCUUGGCGGcacgcUGCGCc -3' miRNA:   3'- -ACUCGCa-----CGGGACCGUCccuu-AUGCG- -5'
21876	5'	-56.8	NC_004902.1	+	4874	0.67	0.469621
	Target:  5'- ------aGCCCUGGCGGGGAcauGUuuGCg -3' miRNA:   3'- acucgcaCGGGACCGUCCCU---UAugCG- -5'
21876	5'	-56.8	NC_004902.1	+	27703	0.68	0.410687
	Target:  5'- aUGGGCGUGCCUcgGGCAacGGGc--AUGUa -3' miRNA:   3'- -ACUCGCACGGGa-CCGU--CCCuuaUGCG- -5'
21876	5'	-56.8	NC_004902.1	+	3163	0.68	0.410687
	Target:  5'- gUGAGCGUauuCCCUGcCAGGGc--ACGCu -3' miRNA:   3'- -ACUCGCAc--GGGACcGUCCCuuaUGCG- -5'
21876	5'	-56.8	NC_004902.1	+	7800	0.69	0.398534
	Target:  5'- aGAGUGcugaaagaucUGUuagaccccguauuuUCUGGCAGGGuGUACGCa -3' miRNA:   3'- aCUCGC----------ACG--------------GGACCGUCCCuUAUGCG- -5'
21876	5'	-56.8	NC_004902.1	+	39619	0.71	0.278001
	Target:  5'- aGGGCcUGCCaaGGCAGGGAGUGuUGCu -3' miRNA:   3'- aCUCGcACGGgaCCGUCCCUUAU-GCG- -5'
21876	5'	-56.8	NC_004902.1	+	3089	1.11	0.000327
	Target:  5'- gUGAGCGUGCCCUGGCAGGGAAUACGCu -3' miRNA:   3'- -ACUCGCACGGGACCGUCCCUUAUGCG- -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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