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
27941	3'	-54.1	NC_005886.2	+	46725	0.66	0.712851
	Target:  5'- uGCCAuGGUGCaucacaugCGGCGGGcuggUgGAACAc -3' miRNA:   3'- cCGGU-CUACGa-------GCCGCCCa---AgUUUGU- -5'
27941	3'	-54.1	NC_005886.2	+	30550	0.66	0.712851
	Target:  5'- -aCCAGAUGUacCGGUGGGUUU--GCGg -3' miRNA:   3'- ccGGUCUACGa-GCCGCCCAAGuuUGU- -5'
27941	3'	-54.1	NC_005886.2	+	40029	0.66	0.700754
	Target:  5'- gGGCCAugcugaugccggcGAUGUUCGGCaGGU-CGAAg- -3' miRNA:   3'- -CCGGU-------------CUACGAGCCGcCCAaGUUUgu -5'
27941	3'	-54.1	NC_005886.2	+	39733	0.69	0.567648
	Target:  5'- cGCCuGAUGCgcgUGGCGGag-CAAACGa -3' miRNA:   3'- cCGGuCUACGa--GCCGCCcaaGUUUGU- -5'
27941	3'	-54.1	NC_005886.2	+	31112	0.73	0.339698
	Target:  5'- aGGUCGGAagcuUGC-CGGCcgcaaaGGGUUCAAGCGu -3' miRNA:   3'- -CCGGUCU----ACGaGCCG------CCCAAGUUUGU- -5'
27941	3'	-54.1	NC_005886.2	+	21086	0.8	0.115005
	Target:  5'- cGGCCccuaAGAUGCUCGGCacugugccuaccGGGUUCAAuaGCAc -3' miRNA:   3'- -CCGG----UCUACGAGCCG------------CCCAAGUU--UGU- -5'
27941	3'	-54.1	NC_005886.2	+	29629	1.12	0.000696
	Target:  5'- cGGCCAGAUGCUCGGCGGGUUCAAACAa -3' miRNA:   3'- -CCGGUCUACGAGCCGCCCAAGUUUGU- -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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