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
12519	3'	-51.6	NC_003345.1	+	70519	0.66	0.942026
	Target:  5'- gGGGAACGGGACGguacugaacucUCGAaucugcCCGUCg- -3' miRNA:   3'- -UCCUUGUCCUGCa----------AGCUgu----GGUAGac -5'
12519	3'	-51.6	NC_003345.1	+	24499	0.67	0.9007
	Target:  5'- gAGGAGCuGGugGacUUGACACCAg--- -3' miRNA:   3'- -UCCUUGuCCugCa-AGCUGUGGUagac -5'
12519	3'	-51.6	NC_003345.1	+	58837	0.68	0.878922
	Target:  5'- aAGGGugGGGACGUU-GGCgaGCUAUCg- -3' miRNA:   3'- -UCCUugUCCUGCAAgCUG--UGGUAGac -5'
12519	3'	-51.6	NC_003345.1	+	37927	0.68	0.871147
	Target:  5'- uAGGGACgagGGGAUGUUCcGC-CCGUCUu -3' miRNA:   3'- -UCCUUG---UCCUGCAAGcUGuGGUAGAc -5'
12519	3'	-51.6	NC_003345.1	+	68738	0.69	0.80927
	Target:  5'- cGGGAugcgcucGCAGGACGUUCGugAgCAg--- -3' miRNA:   3'- -UCCU-------UGUCCUGCAAGCugUgGUagac -5'
12519	3'	-51.6	NC_003345.1	+	36622	0.71	0.7475
	Target:  5'- cGGGcggugacugaccacAACGGGaACGUUUGugGCUAUCUGu -3' miRNA:   3'- -UCC--------------UUGUCC-UGCAAGCugUGGUAGAC- -5'
12519	3'	-51.6	NC_003345.1	+	12882	1.08	0.004053
	Target:  5'- cAGGAACAGGACGUUCGACACCAUCUGu -3' miRNA:   3'- -UCCUUGUCCUGCAAGCUGUGGUAGAC- -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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