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
2352	3'	-59.3	NC_001416.1	+	3107	0.66	0.441578
	Target:  5'- aGCUGGau-GGCGUUGGCGGCa---- -3' miRNA:   3'- gCGACCgcgUCGCAGCCGUCGaaguc -5'
2352	3'	-59.3	NC_001416.1	+	18356	0.66	0.440613
	Target:  5'- cCGCUGGUaauggugGgGGcCGUCaGGC-GCUUCAGg -3' miRNA:   3'- -GCGACCG-------CgUC-GCAG-CCGuCGAAGUC- -5'
2352	3'	-59.3	NC_001416.1	+	16855	0.67	0.400304
	Target:  5'- uGCUGGaaaCGCagaccguggauuucAGCGUCGGCgcagaagGGCUUCGc -3' miRNA:   3'- gCGACC---GCG--------------UCGCAGCCG-------UCGAAGUc -5'
2352	3'	-59.3	NC_001416.1	+	12669	0.69	0.303272
	Target:  5'- gGC-GGCGCAuccGCGUCaGGCGGUacagccaUUCAGg -3' miRNA:   3'- gCGaCCGCGU---CGCAG-CCGUCG-------AAGUC- -5'
2352	3'	-59.3	NC_001416.1	+	12198	0.72	0.186372
	Target:  5'- gCGCUGGCGCAGCa--GGCGGauaaaUUCGc -3' miRNA:   3'- -GCGACCGCGUCGcagCCGUCg----AAGUc -5'
2352	3'	-59.3	NC_001416.1	+	6753	0.73	0.158541
	Target:  5'- cCGCUGGCGUucAGCG-CGuaGGCUUCGa -3' miRNA:   3'- -GCGACCGCG--UCGCaGCcgUCGAAGUc -5'
2352	3'	-59.3	NC_001416.1	+	17242	1.07	0.000406
	Target:  5'- uCGCUGGCGCAGCGUCGGCAGCUUCAGc -3' miRNA:   3'- -GCGACCGCGUCGCAGCCGUCGAAGUC- -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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