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
28513	3'	-54.3	NC_005946.1	+	11420	0.66	0.899037
	Target:  5'- cGGCUACAGCCcuGGCCa-ACAuguacGUCg- -3' miRNA:   3'- -CCGAUGUCGG--CCGGagUGUua---CAGac -5'
28513	3'	-54.3	NC_005946.1	+	7790	0.68	0.801919
	Target:  5'- gGGCgACGGUCauguagacguuGGCCUCgACGGUGUCg- -3' miRNA:   3'- -CCGaUGUCGG-----------CCGGAG-UGUUACAGac -5'
28513	3'	-54.3	NC_005946.1	+	17690	0.68	0.792537
	Target:  5'- cGCU-CGGa-GGCUUCACGGUGUUUGg -3' miRNA:   3'- cCGAuGUCggCCGGAGUGUUACAGAC- -5'
28513	3'	-54.3	NC_005946.1	+	66496	0.68	0.782997
	Target:  5'- aGGCgUACGGCCuugccucuccuaGGCCUgggaGCAagGUCUGa -3' miRNA:   3'- -CCG-AUGUCGG------------CCGGAg---UGUuaCAGAC- -5'
28513	3'	-54.3	NC_005946.1	+	3687	0.69	0.743469
	Target:  5'- aGC-ACAGCuCGGCCUCGuCGGgggcGUCUGc -3' miRNA:   3'- cCGaUGUCG-GCCGGAGU-GUUa---CAGAC- -5'
28513	3'	-54.3	NC_005946.1	+	66089	0.69	0.732274
	Target:  5'- cGGCUGCGG-CGGCCUCucugacuGCucUGUCa- -3' miRNA:   3'- -CCGAUGUCgGCCGGAG-------UGuuACAGac -5'
28513	3'	-54.3	NC_005946.1	+	38381	0.71	0.659999
	Target:  5'- aGGCga-AGCCGGCCUugacCAgGAcGUCUGa -3' miRNA:   3'- -CCGaugUCGGCCGGA----GUgUUaCAGAC- -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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