miRNA display CGI

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Acc. No.	Name	Perfect MFE.*	RefSeq Acc.	strand	Start Position	R_P_ratio#	P value
	Predicted miRNA align pattern
MIMAT0002179	kshv-miR-K12-10a	-51.9	NC_003409.1	-	25906	0.66	0.943578
	Target:  5'- --gACUUaGGGGGACAGCGCg- -3' miRNA:   3'- cggUGAGcCCCCCUGUUGUGau -5'
MIMAT0002179	kshv-miR-K12-10a	-51.9	NC_003409.1	-	52159	0.66	0.942093
	Target:  5'- aGUCGCaCGGGGGGugGccuguggcgugugcGCGCUGg -3' miRNA:   3'- -CGGUGaGCCCCCCugU--------------UGUGAU- -5'
MIMAT0002179	kshv-miR-K12-10a	-51.9	NC_003409.1	+	127711	0.67	0.921697
	Target:  5'- uGCUGCUCuuGGGGACGugACUGc -3' miRNA:   3'- -CGGUGAGccCCCCUGUugUGAU- -5'
MIMAT0002179	kshv-miR-K12-10a	-51.9	NC_003409.1	+	88387	0.7	0.771786
	Target:  5'- -gCAUUgGGGGGGACAacagACACUGa -3' miRNA:   3'- cgGUGAgCCCCCCUGU----UGUGAU- -5'
MIMAT0002179	kshv-miR-K12-10a	-51.9	NC_003409.1	+	70884	0.7	0.751102
	Target:  5'- --aGCUUGGGGGGGCAgagaugGCGCUAc -3' miRNA:   3'- cggUGAGCCCCCCUGU------UGUGAU- -5'
MIMAT0002179	kshv-miR-K12-10a	-51.9	NC_003409.1	-	19292	0.71	0.708343
	Target:  5'- cGCCACgUGGGGcGGGCAuACGCUGc -3' miRNA:   3'- -CGGUGaGCCCC-CCUGU-UGUGAU- -5'
MIMAT0002179	kshv-miR-K12-10a	-51.9	NC_003409.1	+	117851	1.01	0.011255
	Target:  5'- gGCCACUCGGGGGGACAACACUAa -3' miRNA:   3'- -CGGUGAGCCCCCCUGUUGUGAU- -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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