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
13535	5'	-42.5	NC_003436.1	+	23562	0.68	0.986395
	Target:  5'- gCAUAGCuaaaagGCAAUGCc-GCUGCA-GCAGu -3' miRNA:   3'- -GUAUCG------UGUUACGaaUGAUGUuUGUC- -5'
13535	5'	-42.5	NC_003436.1	+	11676	0.68	0.984223
	Target:  5'- aGUAGCACugacUGCcggUAUgACAGACAGa -3' miRNA:   3'- gUAUCGUGuu--ACGa--AUGaUGUUUGUC- -5'
13535	5'	-42.5	NC_003436.1	+	23062	0.69	0.979103
	Target:  5'- uGUAGCACAAUcaacACUACAGGCGu -3' miRNA:   3'- gUAUCGUGUUAcgaaUGAUGUUUGUc -5'
13535	5'	-42.5	NC_003436.1	+	5779	0.71	0.934385
	Target:  5'- -cUGGUGCAGUaacaacacGCUUACUACAacAACAGc -3' miRNA:   3'- guAUCGUGUUA--------CGAAUGAUGU--UUGUC- -5'
13535	5'	-42.5	NC_003436.1	+	18589	0.72	0.921089
	Target:  5'- uCAUAGCuauguCAAUGCUUACaACAccuuuacgucAGCGGg -3' miRNA:   3'- -GUAUCGu----GUUACGAAUGaUGU----------UUGUC- -5'
13535	5'	-42.5	NC_003436.1	+	16397	0.74	0.829591
	Target:  5'- uGUGGUAUGAUGCgugaacauuugucaUUGCUAUAAGCAGu -3' miRNA:   3'- gUAUCGUGUUACG--------------AAUGAUGUUUGUC- -5'
13535	5'	-42.5	NC_003436.1	+	18614	1.11	0.007496
	Target:  5'- aCAUAGCACAAUGCUUACUACAAACAGc -3' miRNA:   3'- -GUAUCGUGUUACGAAUGAUGUUUGUC- -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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