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
4369	3'	-54.4	NC_001720.1	+	20116	0.65	0.708462
	Target:  5'- cUUGGGCGCCAAGaacgcucucuacaaCGUuccggccggcuccacGcUGCUGACCa -3' miRNA:   3'- -AGCUCGCGGUUCg-------------GUA---------------CuACGACUGG- -5'
4369	3'	-54.4	NC_001720.1	+	12458	0.66	0.688443
	Target:  5'- cCGcGCGgCGAGCCAcGGUGCccgaGAUCa -3' miRNA:   3'- aGCuCGCgGUUCGGUaCUACGa---CUGG- -5'
4369	3'	-54.4	NC_001720.1	+	42309	0.66	0.677237
	Target:  5'- -aGAGCGUacagcaGGGCCucuugcUGGUGCUG-CCu -3' miRNA:   3'- agCUCGCGg-----UUCGGu-----ACUACGACuGG- -5'
4369	3'	-54.4	NC_001720.1	+	15802	0.66	0.665986
	Target:  5'- -aGGGCGgCGAGCgCGUGAcagUGACCa -3' miRNA:   3'- agCUCGCgGUUCG-GUACUacgACUGG- -5'
4369	3'	-54.4	NC_001720.1	+	25783	0.66	0.665986
	Target:  5'- cCG-GCGCCGGcGCCGcgGGUGCggcgGGCg -3' miRNA:   3'- aGCuCGCGGUU-CGGUa-CUACGa---CUGg -5'
4369	3'	-54.4	NC_001720.1	+	18050	0.67	0.619628
	Target:  5'- uUCG-GCGCC-AGCCGUccccguaGAcgUGCcGACCa -3' miRNA:   3'- -AGCuCGCGGuUCGGUA-------CU--ACGaCUGG- -5'
4369	3'	-54.4	NC_001720.1	+	24379	1.13	0.000416
	Target:  5'- uUCGAGCGCCAAGCCAUGAUGCUGACCg -3' miRNA:   3'- -AGCUCGCGGUUCGGUACUACGACUGG- -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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