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
18184	5'	-50.5	NC_004680.1	+	56574	0.66	0.942931
	Target:  5'- gCgUGUUGAGUUUG-CGgCGGUGAUCGUc -3' miRNA:   3'- -GgGCAACUCAAGCuGC-GUCAUUGGUA- -5'
18184	5'	-50.5	NC_004680.1	+	37128	0.66	0.937769
	Target:  5'- aCCGacGAGUUugUGugGcCGGUAACCAa -3' miRNA:   3'- gGGCaaCUCAA--GCugC-GUCAUUGGUa -5'
18184	5'	-50.5	NC_004680.1	+	43209	0.67	0.899999
	Target:  5'- gCCGUUcGuGUggucggcacuucaUCGGCGuCAGUGACCAc -3' miRNA:   3'- gGGCAA-CuCA-------------AGCUGC-GUCAUUGGUa -5'
18184	5'	-50.5	NC_004680.1	+	42136	0.68	0.878325
	Target:  5'- cCCCGUUGAGguggagaaggUGGCGUGGcUGACCc- -3' miRNA:   3'- -GGGCAACUCaa--------GCUGCGUC-AUUGGua -5'
18184	5'	-50.5	NC_004680.1	+	42842	0.72	0.691288
	Target:  5'- cCCUGUUGAGgacaagcacgCGugGC-GUGACCAa -3' miRNA:   3'- -GGGCAACUCaa--------GCugCGuCAUUGGUa -5'
18184	5'	-50.5	NC_004680.1	+	21229	0.73	0.62265
	Target:  5'- gCCGguggauaUUGGGUUCGAUGCAGUGucgucgGCCGg -3' miRNA:   3'- gGGC-------AACUCAAGCUGCGUCAU------UGGUa -5'
18184	5'	-50.5	NC_004680.1	+	22406	1.09	0.003764
	Target:  5'- uCCCGUUGAGUUCGACGCAGUAACCAUg -3' miRNA:   3'- -GGGCAACUCAAGCUGCGUCAUUGGUA- -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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