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
4360	5'	-61.6	NC_001720.1	+	3933	0.66	0.346953
	Target:  5'- gGAGUugauucGGCUGUCGGAGA-UCGCgaGCg -3' miRNA:   3'- gUUCA------CCGACGGCCUCUcGGCGggCG- -5'
4360	5'	-61.6	NC_001720.1	+	5576	0.66	0.338864
	Target:  5'- gGGGUGG-UGCCGaGAcccGAGUC-CCCGCc -3' miRNA:   3'- gUUCACCgACGGC-CU---CUCGGcGGGCG- -5'
4360	5'	-61.6	NC_001720.1	+	26532	0.67	0.277062
	Target:  5'- -cGG-GGgUGCCGGAcgaggcggcugcgcGAGCCGCCuCGg -3' miRNA:   3'- guUCaCCgACGGCCU--------------CUCGGCGG-GCg -5'
4360	5'	-61.6	NC_001720.1	+	17771	0.68	0.246236
	Target:  5'- gCAAcGUGGCUaauuugGCCGGAGAGaCGCUgGg -3' miRNA:   3'- -GUU-CACCGA------CGGCCUCUCgGCGGgCg -5'
4360	5'	-61.6	NC_001720.1	+	13045	0.69	0.188612
	Target:  5'- aCGAG-GGgUGCCGuGAGccugacguucaacaAGCCGUCCGUg -3' miRNA:   3'- -GUUCaCCgACGGC-CUC--------------UCGGCGGGCG- -5'
4360	5'	-61.6	NC_001720.1	+	29298	0.7	0.175604
	Target:  5'- ----aGGcCUGCCGGAG-GCCGCCaGUu -3' miRNA:   3'- guucaCC-GACGGCCUCuCGGCGGgCG- -5'
4360	5'	-61.6	NC_001720.1	+	17931	1.09	0.00016
	Target:  5'- gCAAGUGGCUGCCGGAGAGCCGCCCGCc -3' miRNA:   3'- -GUUCACCGACGGCCUCUCGGCGGGCG- -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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