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
12028	3'	-56.7	NC_003278.1	+	35083	0.66	0.534426
	Target:  5'- aUCCgGCUguugCCcUGGGACGGcagguuugacggcaGGCUUCCa -3' miRNA:   3'- -AGG-CGAa---GGuACCUUGCC--------------UCGGAGGg -5'
12028	3'	-56.7	NC_003278.1	+	13172	0.67	0.474082
	Target:  5'- gCCGUUgUCGUGGuGACGGugcaGGCCgCCCa -3' miRNA:   3'- aGGCGAaGGUACC-UUGCC----UCGGaGGG- -5'
12028	3'	-56.7	NC_003278.1	+	2314	0.67	0.463842
	Target:  5'- gCCGCUgUCUAUGGA--GGGGCUggCCa -3' miRNA:   3'- aGGCGA-AGGUACCUugCCUCGGagGG- -5'
12028	3'	-56.7	NC_003278.1	+	11980	0.67	0.463842
	Target:  5'- cCUGCUcgUUCA-GGGugGGGGCgUUCCa -3' miRNA:   3'- aGGCGA--AGGUaCCUugCCUCGgAGGG- -5'
12028	3'	-56.7	NC_003278.1	+	8679	0.67	0.453719
	Target:  5'- gCCGCcaCCGaGGAcGCGGugcguGCCUUCCa -3' miRNA:   3'- aGGCGaaGGUaCCU-UGCCu----CGGAGGG- -5'
12028	3'	-56.7	NC_003278.1	+	25847	0.67	0.447703
	Target:  5'- uUCUGCUUCUggcacgcgggccuauGUGaaGAAUGGGGUaCUCCCg -3' miRNA:   3'- -AGGCGAAGG---------------UAC--CUUGCCUCG-GAGGG- -5'
12028	3'	-56.7	NC_003278.1	+	31799	1.13	0.000219
	Target:  5'- aUCCGCUUCCAUGGAACGGAGCCUCCCg -3' miRNA:   3'- -AGGCGAAGGUACCUUGCCUCGGAGGG- -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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