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
13567	5'	-55.2	NC_003444.1	+	31989	0.66	0.598202
	Target:  5'- aGGcaGUGAuccgucgUGCUGGUGGCGuGGAAUg-- -3' miRNA:   3'- aCC--UACU-------ACGACCACCGU-CCUUGgcu -5'
13567	5'	-55.2	NC_003444.1	+	35471	0.67	0.506732
	Target:  5'- cGGAUGGccuaaaucgcuuucUGUugccauuggUGGUGGCGuGGGGCUGAu -3' miRNA:   3'- aCCUACU--------------ACG---------ACCACCGU-CCUUGGCU- -5'
13567	5'	-55.2	NC_003444.1	+	16565	0.67	0.499174
	Target:  5'- -aGGUGGUGUUGGUGGCA---GCUGGc -3' miRNA:   3'- acCUACUACGACCACCGUccuUGGCU- -5'
13567	5'	-55.2	NC_003444.1	+	9880	0.68	0.450854
	Target:  5'- aGGGUGG-GCUGGcgcuugguggcggacUGGCAgcGGGGCUGAc -3' miRNA:   3'- aCCUACUaCGACC---------------ACCGU--CCUUGGCU- -5'
13567	5'	-55.2	NC_003444.1	+	35380	0.7	0.343341
	Target:  5'- uUGGc-GGUGgUGGUGGCuGGAAgCGAa -3' miRNA:   3'- -ACCuaCUACgACCACCGuCCUUgGCU- -5'
13567	5'	-55.2	NC_003444.1	+	30846	0.74	0.207883
	Target:  5'- -aGGUGAaaagaaUGCUGGUGGaguGGGGACCGGu -3' miRNA:   3'- acCUACU------ACGACCACCg--UCCUUGGCU- -5'
13567	5'	-55.2	NC_003444.1	+	32458	1.09	0.000527
	Target:  5'- cUGGAUGAUGCUGGUGGCAGGAACCGAa -3' miRNA:   3'- -ACCUACUACGACCACCGUCCUUGGCU- -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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