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
27269	3'	-45.2	NC_005841.1	+	23576	0.66	0.992871
	Target:  5'- -uGCcGGAgcaUAACGaAUGGCAaagACGAAGUg -3' miRNA:   3'- guUGaCCU---AUUGC-UACCGU---UGUUUCA- -5'
27269	3'	-45.2	NC_005841.1	+	23716	0.67	0.982605
	Target:  5'- gCGGCgGGAaugagaugcUGGCGggGGCAACAcAGUc -3' miRNA:   3'- -GUUGaCCU---------AUUGCuaCCGUUGUuUCA- -5'
27269	3'	-45.2	NC_005841.1	+	17773	0.68	0.97744
	Target:  5'- uUAACUGGcaugGACGAUGGCuuGACGcugaaagcuggAAGUg -3' miRNA:   3'- -GUUGACCua--UUGCUACCG--UUGU-----------UUCA- -5'
27269	3'	-45.2	NC_005841.1	+	19566	0.68	0.97447
	Target:  5'- uUAACUGGuucuGCaGGUGGCGcaACGAAGa -3' miRNA:   3'- -GUUGACCuau-UG-CUACCGU--UGUUUCa -5'
27269	3'	-45.2	NC_005841.1	+	13207	0.69	0.963867
	Target:  5'- gCAGCUaggugGGGUGGCGAUGGU---GAGGUg -3' miRNA:   3'- -GUUGA-----CCUAUUGCUACCGuugUUUCA- -5'
27269	3'	-45.2	NC_005841.1	+	22325	0.71	0.914879
	Target:  5'- gCAACUGGAgagaguucGACGGUGGCAuCAuuGc -3' miRNA:   3'- -GUUGACCUa-------UUGCUACCGUuGUuuCa -5'
27269	3'	-45.2	NC_005841.1	+	6255	0.77	0.610031
	Target:  5'- gGGCUGGA---CGAUGGCGACAucGUu -3' miRNA:   3'- gUUGACCUauuGCUACCGUUGUuuCA- -5'
27269	3'	-45.2	NC_005841.1	+	30171	1.08	0.009027
	Target:  5'- gCAACUGGAUAACGAUGGCAACAAAGUu -3' miRNA:   3'- -GUUGACCUAUUGCUACCGUUGUUUCA- -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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