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
31786	3'	-58.3	NC_006938.1	+	2146	1.08	0.000626
	Target:  5'- cGUCAACUGGGGCGACGUGCACGCCUCc -3' miRNA:   3'- -CAGUUGACCCCGCUGCACGUGCGGAG- -5'
31786	3'	-58.3	NC_006938.1	+	2199	0.69	0.410756
	Target:  5'- -cCAACUGGGGCGAgggcggcaucauagaCGUGCuccgGCCa- -3' miRNA:   3'- caGUUGACCCCGCU---------------GCACGug--CGGag -5'
31786	3'	-58.3	NC_006938.1	+	29290	0.68	0.463695
	Target:  5'- uGUCAG-UGuGGCGugGUGCgccuGCGUCUCg -3' miRNA:   3'- -CAGUUgACcCCGCugCACG----UGCGGAG- -5'
31786	3'	-58.3	NC_006938.1	+	35806	0.68	0.473522
	Target:  5'- -cCAGCUGGacgGGCGACacgGUGCGCaguGCCUg -3' miRNA:   3'- caGUUGACC---CCGCUG---CACGUG---CGGAg -5'
31786	3'	-58.3	NC_006938.1	+	41592	0.67	0.483453
	Target:  5'- cGUCAGCaGGGaGCGGC-UGCGCggcgGCCUg -3' miRNA:   3'- -CAGUUGaCCC-CGCUGcACGUG----CGGAg -5'
31786	3'	-58.3	NC_006938.1	+	46669	0.67	0.493482
	Target:  5'- -gCAGCUGGGGagcgcggGGcCGUGU-CGCCUCu -3' miRNA:   3'- caGUUGACCCCg------CU-GCACGuGCGGAG- -5'
31786	3'	-58.3	NC_006938.1	+	60618	0.66	0.544937
	Target:  5'- -cCAACUucgccaucGGGGCGGCGaGCuccauCGUCUCu -3' miRNA:   3'- caGUUGA--------CCCCGCUGCaCGu----GCGGAG- -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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