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
29191	5'	-56.9	NC_006150.1	+	122305	0.66	0.943109
	Target:  5'- cGGGCGGCGgaGGAaucauucuCCGUacuaucucugccaCAUCgggGUGg -3' miRNA:   3'- -CCCGCCGCaaCCU--------GGCG-------------GUAGaa-CAC- -5'
29191	5'	-56.9	NC_006150.1	+	109362	0.66	0.939074
	Target:  5'- aGGUGGCcaaucGGGCCGUCAUCUg--- -3' miRNA:   3'- cCCGCCGcaa--CCUGGCGGUAGAacac -5'
29191	5'	-56.9	NC_006150.1	+	219758	0.66	0.933897
	Target:  5'- cGGCGGCGgcaGGACCuggcgugGCCG-CggGUGg -3' miRNA:   3'- cCCGCCGCaa-CCUGG-------CGGUaGaaCAC- -5'
29191	5'	-56.9	NC_006150.1	+	70940	0.67	0.907561
	Target:  5'- aGGGCGGCGgaGcGAUCGUCAUUc---- -3' miRNA:   3'- -CCCGCCGCaaC-CUGGCGGUAGaacac -5'
29191	5'	-56.9	NC_006150.1	+	12921	0.71	0.741754
	Target:  5'- cGGCGGuCGUUcGGugCGUUGUCgUUGUGg -3' miRNA:   3'- cCCGCC-GCAA-CCugGCGGUAG-AACAC- -5'
29191	5'	-56.9	NC_006150.1	+	69730	0.73	0.624867
	Target:  5'- aGGCGGUGUUGGGCCucaacGCCGcg-UGUGc -3' miRNA:   3'- cCCGCCGCAACCUGG-----CGGUagaACAC- -5'
29191	5'	-56.9	NC_006150.1	+	107714	1.11	0.002641
	Target:  5'- cGGGCGGCGUUGGACCGCCAUCUUGUGg -3' miRNA:   3'- -CCCGCCGCAACCUGGCGGUAGAACAC- -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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