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
2873	5'	-52.1	NC_001493.1	+	38257	0.66	0.95945
	Target:  5'- cGAGUaagAUCGUCAACUGCACCc--- -3' miRNA:   3'- -UUCAgagUAGCAGUUGGCGUGGcuau -5'
2873	5'	-52.1	NC_001493.1	+	57429	0.67	0.946934
	Target:  5'- -cGUUUCcgggcacccGUCGUC-GCCGUGCCGGUAg -3' miRNA:   3'- uuCAGAG---------UAGCAGuUGGCGUGGCUAU- -5'
2873	5'	-52.1	NC_001493.1	+	102575	0.67	0.942252
	Target:  5'- -cGUCUCcacaugUGUUcGCCGUACCGAUGc -3' miRNA:   3'- uuCAGAGua----GCAGuUGGCGUGGCUAU- -5'
2873	5'	-52.1	NC_001493.1	+	39332	0.69	0.881061
	Target:  5'- uGGUCguaGUCGUUGACCGCgguACCGGUc -3' miRNA:   3'- uUCAGag-UAGCAGUUGGCG---UGGCUAu -5'
2873	5'	-52.1	NC_001493.1	+	81972	0.7	0.865782
	Target:  5'- cGAGUUUguUCGUCGAuuCCGCcCCGGUGa -3' miRNA:   3'- -UUCAGAguAGCAGUU--GGCGuGGCUAU- -5'
2873	5'	-52.1	NC_001493.1	+	130250	0.71	0.805401
	Target:  5'- cGGUC-CGUCGUCcGCCGCGCUGc-- -3' miRNA:   3'- uUCAGaGUAGCAGuUGGCGUGGCuau -5'
2873	5'	-52.1	NC_001493.1	+	120816	1.04	0.009799
	Target:  5'- gAAGUCUCAUCGUCAACCGCACCGAUAc -3' miRNA:   3'- -UUCAGAGUAGCAGUUGGCGUGGCUAU- -5'
2873	5'	-52.1	NC_001493.1	+	5262	1.04	0.009799
	Target:  5'- gAAGUCUCAUCGUCAACCGCACCGAUAc -3' miRNA:   3'- -UUCAGAGUAGCAGUUGGCGUGGCUAU- -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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