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
30726	5'	-52.5	NC_006552.1	+	61724	0.66	0.868293
	Target:  5'- cGCGGGua-CGCGCCCUGgccgaaguccUACAUCGAc -3' miRNA:   3'- -UGUUCuggGUGUGGGAC----------AUGUAGCUu -5'
30726	5'	-52.5	NC_006552.1	+	60266	0.66	0.863349
	Target:  5'- cGCGGGcuuuCCCGCcgcgccacccggcugGCCCUGgGCAUCGGc -3' miRNA:   3'- -UGUUCu---GGGUG---------------UGGGACaUGUAGCUu -5'
30726	5'	-52.5	NC_006552.1	+	61967	0.67	0.833673
	Target:  5'- gACcAGAUCCaauGCGCCgCUGUGCAgcagCGAGg -3' miRNA:   3'- -UGuUCUGGG---UGUGG-GACAUGUa---GCUU- -5'
30726	5'	-52.5	NC_006552.1	+	20437	0.68	0.78551
	Target:  5'- uCGAGGgCCAgGCCCUGcUGCAcggCGAAg -3' miRNA:   3'- uGUUCUgGGUgUGGGAC-AUGUa--GCUU- -5'
30726	5'	-52.5	NC_006552.1	+	59057	0.71	0.588468
	Target:  5'- cACGAGGCUgGCGCUCUGcGCGUCGc- -3' miRNA:   3'- -UGUUCUGGgUGUGGGACaUGUAGCuu -5'
30726	5'	-52.5	NC_006552.1	+	54001	0.71	0.566212
	Target:  5'- cGCGuGGCCCugGCCCUG-GCcgCGAGc -3' miRNA:   3'- -UGUuCUGGGugUGGGACaUGuaGCUU- -5'
30726	5'	-52.5	NC_006552.1	+	50784	1.06	0.003292
	Target:  5'- gACAAGACCCACACCCUGUACAUCGAAc -3' miRNA:   3'- -UGUUCUGGGUGUGGGACAUGUAGCUU- -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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