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
1262	3'	-54.6	NC_001317.1	+	5166	0.67	0.489436
	Target:  5'- cGCCUCgaccugugggcGCGUUUUCAGgAcuUUCAGCGUc -3' miRNA:   3'- -CGGAG-----------UGCAGGAGUCgU--AAGUCGCGu -5'
1262	3'	-54.6	NC_001317.1	+	9737	0.69	0.368761
	Target:  5'- uGCCUCugGUCUUUAGCcgcgccaaaUCAcGCGCc -3' miRNA:   3'- -CGGAGugCAGGAGUCGua-------AGU-CGCGu -5'
1262	3'	-54.6	NC_001317.1	+	10568	0.67	0.478646
	Target:  5'- aGCCUgaGCG-CCggguuuugCGGCAUaucaaUCAGCGCAg -3' miRNA:   3'- -CGGAg-UGCaGGa-------GUCGUA-----AGUCGCGU- -5'
1262	3'	-54.6	NC_001317.1	+	11338	1.1	0.000388
	Target:  5'- gGCCUCACGUCCUCAGCAUUCAGCGCAu -3' miRNA:   3'- -CGGAGUGCAGGAGUCGUAAGUCGCGU- -5'
1262	3'	-54.6	NC_001317.1	+	12821	0.67	0.478646
	Target:  5'- -gCUCGCGUCCUgAGCGguauaUUUAGCauuaGCAa -3' miRNA:   3'- cgGAGUGCAGGAgUCGU-----AAGUCG----CGU- -5'
1262	3'	-54.6	NC_001317.1	+	13929	0.67	0.511346
	Target:  5'- uGCCUC-CG-CCUCAGCAagaAGUGUu -3' miRNA:   3'- -CGGAGuGCaGGAGUCGUaagUCGCGu -5'
1262	3'	-54.6	NC_001317.1	+	28057	0.69	0.378017
	Target:  5'- uGCCUUuuuccgggucaAUGgCCUCAGCAUggaAGCGCGc -3' miRNA:   3'- -CGGAG-----------UGCaGGAGUCGUAag-UCGCGU- -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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