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
32037	3'	-48.5	NC_006953.1	+	29865	0.66	0.920519
	Target:  5'- uUGCGCAUGUUGaaUGGUGGCGGc---- -3' miRNA:   3'- -ACGCGUGCAAUa-ACUACUGCUaccag -5'
32037	3'	-48.5	NC_006953.1	+	15322	0.66	0.920519
	Target:  5'- uUGCGC-CGUUGU-GAUGGuCGAUGa-- -3' miRNA:   3'- -ACGCGuGCAAUAaCUACU-GCUACcag -5'
32037	3'	-48.5	NC_006953.1	+	28230	0.67	0.913838
	Target:  5'- cGCGCAUcugUAUgUGAUGGCGGUcacGGUUu -3' miRNA:   3'- aCGCGUGca-AUA-ACUACUGCUA---CCAG- -5'
32037	3'	-48.5	NC_006953.1	+	1138	0.67	0.891877
	Target:  5'- gUGCGCACGUUGgaugcaaGAUGAUGugcGG-Ca -3' miRNA:   3'- -ACGCGUGCAAUaa-----CUACUGCua-CCaG- -5'
32037	3'	-48.5	NC_006953.1	+	785	0.67	0.887147
	Target:  5'- uUGCGCuguaugugaacgacgGCGUUAUUGAgucgguagUGGCuacgGAUGGUUa -3' miRNA:   3'- -ACGCG---------------UGCAAUAACU--------ACUG----CUACCAG- -5'
32037	3'	-48.5	NC_006953.1	+	3875	0.68	0.849207
	Target:  5'- aGCGCauugACGgUAUUGAUGACGcuaaGGUUu -3' miRNA:   3'- aCGCG----UGCaAUAACUACUGCua--CCAG- -5'
32037	3'	-48.5	NC_006953.1	+	15226	1.12	0.002032
	Target:  5'- cUGCGCACGUUAUUGAUGACGAUGGUCa -3' miRNA:   3'- -ACGCGUGCAAUAACUACUGCUACCAG- -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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