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
1520	5'	-60.7	NC_001335.1	+	27026	0.67	0.328828
	Target:  5'- gUGACgaugGGUCUcguaGGCGAAGCCgGCGAg -3' miRNA:   3'- aACUG----CCGGAc---CCGCUUCGGaCGCUa -5'
1520	5'	-60.7	NC_001335.1	+	9480	0.67	0.320946
	Target:  5'- -cGGCGGCgcaUGGGaaGAGGCCaUGCGGa -3' miRNA:   3'- aaCUGCCGg--ACCCg-CUUCGG-ACGCUa -5'
1520	5'	-60.7	NC_001335.1	+	49459	0.67	0.313205
	Target:  5'- gUUGAUGGCUcggUGGGC--AGCCUcGCGGa -3' miRNA:   3'- -AACUGCCGG---ACCCGcuUCGGA-CGCUa -5'
1520	5'	-60.7	NC_001335.1	+	13849	0.67	0.298152
	Target:  5'- aUGGCGGCUcGGGUGAggauguaaguGGCCUcCGGUg -3' miRNA:   3'- aACUGCCGGaCCCGCU----------UCGGAcGCUA- -5'
1520	5'	-60.7	NC_001335.1	+	30307	0.67	0.298152
	Target:  5'- -gGACGaaGCCUGGGUGguGCCgGUGGa -3' miRNA:   3'- aaCUGC--CGGACCCGCuuCGGaCGCUa -5'
1520	5'	-60.7	NC_001335.1	+	8684	0.71	0.149582
	Target:  5'- -cGACGGCCUGgcgcucGGCGAcugagucgacguagAGCCUGgGGUa -3' miRNA:   3'- aaCUGCCGGAC------CCGCU--------------UCGGACgCUA- -5'
1520	5'	-60.7	NC_001335.1	+	46463	1.02	0.00063
	Target:  5'- cUUGACGGCCUGGGCGAAGCCUGCGAUc -3' miRNA:   3'- -AACUGCCGGACCCGCUUCGGACGCUA- -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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