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
18662	5'	-56.8	NC_004682.1	+	40126	0.66	0.630203
	Target:  5'- uGgcGUGGUGCUccUUGCcUGCGGCa-- -3' miRNA:   3'- cCuuCACCACGA--AGCGuGCGCCGgac -5'
18662	5'	-56.8	NC_004682.1	+	25583	0.66	0.597322
	Target:  5'- cGGcuGaGGUGUgugCGCugGCGGCUg- -3' miRNA:   3'- -CCuuCaCCACGaa-GCGugCGCCGGac -5'
18662	5'	-56.8	NC_004682.1	+	46231	0.66	0.579878
	Target:  5'- cGAGGUcgaagccuuggccucGGUGCUgcugUCGCucggcgcugccgACGCGGCCa- -3' miRNA:   3'- cCUUCA---------------CCACGA----AGCG------------UGCGCCGGac -5'
18662	5'	-56.8	NC_004682.1	+	594	0.68	0.490814
	Target:  5'- cGGAGacaGGUGCUcCGUgACGCGGgCUGg -3' miRNA:   3'- -CCUUca-CCACGAaGCG-UGCGCCgGAC- -5'
18662	5'	-56.8	NC_004682.1	+	13383	0.69	0.403085
	Target:  5'- uGGAcgcAGUGGUGC-UCGCucuCGCcGGUCUc -3' miRNA:   3'- -CCU---UCACCACGaAGCGu--GCG-CCGGAc -5'
18662	5'	-56.8	NC_004682.1	+	5459	0.77	0.122581
	Target:  5'- uGAAGUGGgccgGCaUCG-GCGCGGCCUGg -3' miRNA:   3'- cCUUCACCa---CGaAGCgUGCGCCGGAC- -5'
18662	5'	-56.8	NC_004682.1	+	5383	0.96	0.006031
	Target:  5'- gGGAAGUGGUGCUUCGaC-CGCGGCCUGg -3' miRNA:   3'- -CCUUCACCACGAAGC-GuGCGCCGGAC- -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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