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
22180	5'	-57.9	NC_004927.1	+	12904	0.66	0.672586
	Target:  5'- uGGUCGauagaauCACGUCCgUUCAggaaCAGGACg -3' miRNA:   3'- gCCAGCgc-----GUGCAGG-AGGUa---GUCCUG- -5'
22180	5'	-57.9	NC_004927.1	+	46224	0.66	0.693439
	Target:  5'- aGGUCGCGCgguGCGUCaugcgauaCAUCgaccggaggGGGACg -3' miRNA:   3'- gCCAGCGCG---UGCAGgag-----GUAG---------UCCUG- -5'
22180	5'	-57.9	NC_004927.1	+	8306	0.67	0.630536
	Target:  5'- gGGUCGUcuucGUugGaagCCUCgaaGUCGGGACg -3' miRNA:   3'- gCCAGCG----CGugCa--GGAGg--UAGUCCUG- -5'
22180	5'	-57.9	NC_004927.1	+	40909	0.69	0.48668
	Target:  5'- uCGGUaaaGCGCGUCCUUgGUaAGGACg -3' miRNA:   3'- -GCCAgcgCGUGCAGGAGgUAgUCCUG- -5'
22180	5'	-57.9	NC_004927.1	+	29349	0.7	0.448266
	Target:  5'- -cGUCGCcCACGUCuCUCCGucgugguggUCGGGGCu -3' miRNA:   3'- gcCAGCGcGUGCAG-GAGGU---------AGUCCUG- -5'
22180	5'	-57.9	NC_004927.1	+	37877	0.71	0.368458
	Target:  5'- cCGGUCGCGCACcUCCUUguUCAccgcacGGAa -3' miRNA:   3'- -GCCAGCGCGUGcAGGAGguAGU------CCUg -5'
22180	5'	-57.9	NC_004927.1	+	12521	0.71	0.376833
	Target:  5'- uGGUCgaagucuuugGCGU-UGUCCUCCGUCAGcGACu -3' miRNA:   3'- gCCAG----------CGCGuGCAGGAGGUAGUC-CUG- -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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