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
16658	3'	-54.2	NC_004156.1	+	149332	0.66	0.982981
	Target:  5'- gUGGCGUCgguguacgaGGAGGUgguugugUUGGCUguaGUGUGGAa -3' miRNA:   3'- -ACCGUAG---------CCUCCA-------AACUGG---CACGUCU- -5'
16658	3'	-54.2	NC_004156.1	+	138924	0.66	0.981197
	Target:  5'- cGGCcuccUCGGGGGUcaucUUGcACUGUGCGc- -3' miRNA:   3'- aCCGu---AGCCUCCA----AAC-UGGCACGUcu -5'
16658	3'	-54.2	NC_004156.1	+	18322	0.66	0.974234
	Target:  5'- aUGGCcUCGGAGGccaUUG-CCG-GUGGAa -3' miRNA:   3'- -ACCGuAGCCUCCa--AACuGGCaCGUCU- -5'
16658	3'	-54.2	NC_004156.1	+	114838	0.67	0.968354
	Target:  5'- gUGGUGUUGGAGGUagugcuaguggugUUGGuaGUGguGAu -3' miRNA:   3'- -ACCGUAGCCUCCA-------------AACUggCACguCU- -5'
16658	3'	-54.2	NC_004156.1	+	122642	0.69	0.929938
	Target:  5'- cGGCAUCGGGgacauGGUgauuggauuuggaaUGGCCGaUGCAGu -3' miRNA:   3'- aCCGUAGCCU-----CCAa-------------ACUGGC-ACGUCu -5'
16658	3'	-54.2	NC_004156.1	+	127803	0.7	0.871544
	Target:  5'- cGGUGUCGGAGGguaGAgUGUGCcGAu -3' miRNA:   3'- aCCGUAGCCUCCaaaCUgGCACGuCU- -5'
16658	3'	-54.2	NC_004156.1	+	214199	1.09	0.006305
	Target:  5'- cUGGCAUCGGAGGUUUGACCGUGCAGAu -3' miRNA:   3'- -ACCGUAGCCUCCAAACUGGCACGUCU- -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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