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
22072	5'	-55.8	NC_004927.1	+	34024	0.66	0.765595
	Target:  5'- uGAGCCGUGUUCGccuucuuacacggguAGCCGgaGa---- -3' miRNA:   3'- gCUCGGCGCAAGC---------------UCGGCgaCauagu -5'
22072	5'	-55.8	NC_004927.1	+	33742	0.66	0.760624
	Target:  5'- uCGAGCUGUcaaacucgauauaGUUCGAGUCGgUGUcgCc -3' miRNA:   3'- -GCUCGGCG-------------CAAGCUCGGCgACAuaGu -5'
22072	5'	-55.8	NC_004927.1	+	32892	0.66	0.751599
	Target:  5'- uGAGCgGCGUuaUCGAGugacCCGCUGaccuUCGu -3' miRNA:   3'- gCUCGgCGCA--AGCUC----GGCGACau--AGU- -5'
22072	5'	-55.8	NC_004927.1	+	20106	0.71	0.479437
	Target:  5'- -cAGCCGgGUUCGGGCCGUucucggUGUacGUCGg -3' miRNA:   3'- gcUCGGCgCAAGCUCGGCG------ACA--UAGU- -5'
22072	5'	-55.8	NC_004927.1	+	21801	0.73	0.394824
	Target:  5'- gCGAGCCGC--UgGAGCCGCUGg---- -3' miRNA:   3'- -GCUCGGCGcaAgCUCGGCGACauagu -5'
22072	5'	-55.8	NC_004927.1	+	1134	0.76	0.263633
	Target:  5'- aGGGCCG-GUUCGGGCCGCUu--UCAg -3' miRNA:   3'- gCUCGGCgCAAGCUCGGCGAcauAGU- -5'
22072	5'	-55.8	NC_004927.1	+	40156	1.09	0.001277
	Target:  5'- aCGAGCCGCGUUCGAGCCGCUGUAUCAa -3' miRNA:   3'- -GCUCGGCGCAAGCUCGGCGACAUAGU- -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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