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
30306	3'	-49.4	NC_006367.1	+	2749	0.65	0.372617
	Target:  5'- --cGACGGccccGGAUGCAgGGCCGAcccccgaaccccaCGGCg -3' miRNA:   3'- uuuCUGCU----UUUGUGUgCUGGCU-------------GCCG- -5'
30306	3'	-49.4	NC_006367.1	+	4534	0.66	0.331857
	Target:  5'- -cGGAUGcAAGgGCugcuauCGACCGAgCGGCa -3' miRNA:   3'- uuUCUGCuUUUgUGu-----GCUGGCU-GCCG- -5'
30306	3'	-49.4	NC_006367.1	+	806	0.67	0.284536
	Target:  5'- ---cGCGggGACAgACGACUuggGGCGGa -3' miRNA:   3'- uuucUGCuuUUGUgUGCUGG---CUGCCg -5'
30306	3'	-49.4	NC_006367.1	+	1333	0.71	0.168617
	Target:  5'- -uGGugGAGAcCACGCG--UGACGGCa -3' miRNA:   3'- uuUCugCUUUuGUGUGCugGCUGCCG- -5'
30306	3'	-49.4	NC_006367.1	+	2114	0.71	0.151729
	Target:  5'- cGAAGGCGAggucggucgggucGAACugGuCGACgaUGACGGCg -3' miRNA:   3'- -UUUCUGCU-------------UUUGugU-GCUG--GCUGCCG- -5'
30306	3'	-49.4	NC_006367.1	+	3013	0.74	0.096833
	Target:  5'- ---cACaAGAGCgACACGGCCGugGGCa -3' miRNA:   3'- uuucUGcUUUUG-UGUGCUGGCugCCG- -5'
30306	3'	-49.4	NC_006367.1	+	2267	0.74	0.090215
	Target:  5'- cGAAGugcCGGAAACGaa-GACCGAUGGCa -3' miRNA:   3'- -UUUCu--GCUUUUGUgugCUGGCUGCCG- -5'
30306	3'	-49.4	NC_006367.1	+	767	1.11	0.000101
	Target:  5'- gAAAGACGAAAACACACGACCGACGGCg -3' miRNA:   3'- -UUUCUGCUUUUGUGUGCUGGCUGCCG- -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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