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
11178	5'	-53.9	NC_002816.1	+	49294	1.11	0.002499
	Target:  5'- gGCCAACUUGGCGCUCACCUUCCUCACc -3' miRNA:   3'- -CGGUUGAACCGCGAGUGGAAGGAGUG- -5'
11178	5'	-53.9	NC_002816.1	+	45677	0.71	0.716719
	Target:  5'- cGCCGugUUGGCaauuaacacucuccGUUCACCgccuucucgUCCUCAa -3' miRNA:   3'- -CGGUugAACCG--------------CGAGUGGa--------AGGAGUg -5'
11178	5'	-53.9	NC_002816.1	+	80975	0.69	0.807846
	Target:  5'- cGCCAcACUUGGCG-UCG---UCCUCGCa -3' miRNA:   3'- -CGGU-UGAACCGCgAGUggaAGGAGUG- -5'
11178	5'	-53.9	NC_002816.1	+	107391	0.69	0.825778
	Target:  5'- uUCAACUUuGUGCUCACCcaacaccUCCUCAa -3' miRNA:   3'- cGGUUGAAcCGCGAGUGGa------AGGAGUg -5'
11178	5'	-53.9	NC_002816.1	+	6833	0.67	0.882163
	Target:  5'- cCCAACUUGuCGUUCGCUcccuUUCCUCcCg -3' miRNA:   3'- cGGUUGAACcGCGAGUGG----AAGGAGuG- -5'
11178	5'	-53.9	NC_002816.1	+	31631	0.66	0.909283
	Target:  5'- uGCCGucGC-UGGUGUU-GCCguugUCCUCGCg -3' miRNA:   3'- -CGGU--UGaACCGCGAgUGGa---AGGAGUG- -5'
11178	5'	-53.9	NC_002816.1	+	49159	0.66	0.913006
	Target:  5'- cGCCAAgUUGGCcagGUUCGCCgcggcuuugaccgUUUUCACg -3' miRNA:   3'- -CGGUUgAACCG---CGAGUGGa------------AGGAGUG- -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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