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
30724	3'	-59.7	NC_006552.1	+	17649	0.66	0.591271
	Target:  5'- gCGCUGgCGAUCgaguuCGuuGGCGgCGAGGa -3' miRNA:   3'- gGCGACaGCUAG-----GCcuCCGCgGCUCC- -5'
30724	3'	-59.7	NC_006552.1	+	13315	0.66	0.560574
	Target:  5'- gCCuCUGcCGGUUCGGAcuGGgGCCGGGc -3' miRNA:   3'- -GGcGACaGCUAGGCCU--CCgCGGCUCc -5'
30724	3'	-59.7	NC_006552.1	+	20936	0.67	0.500708
	Target:  5'- aCCGUggUGUCGAugUCCGGGcguccGGCaCCGGGa -3' miRNA:   3'- -GGCG--ACAGCU--AGGCCU-----CCGcGGCUCc -5'
30724	3'	-59.7	NC_006552.1	+	63480	0.69	0.390767
	Target:  5'- uCCGCUGcCGG-CCGccGGCGCCGGa- -3' miRNA:   3'- -GGCGACaGCUaGGCcuCCGCGGCUcc -5'
30724	3'	-59.7	NC_006552.1	+	13821	0.71	0.317143
	Target:  5'- gCCGCUGUaGGUgCCGGcgcgcacguucaucAGGCGCCGGuacuGGg -3' miRNA:   3'- -GGCGACAgCUA-GGCC--------------UCCGCGGCU----CC- -5'
30724	3'	-59.7	NC_006552.1	+	3731	0.77	0.137404
	Target:  5'- gUGCUGUCGAggguguUCgCGGGGGCgacaucaaugGCCGAGGa -3' miRNA:   3'- gGCGACAGCU------AG-GCCUCCG----------CGGCUCC- -5'
30724	3'	-59.7	NC_006552.1	+	52046	1.12	0.00038
	Target:  5'- gCCGCUGUCGAUCCGGAGGCGCCGAGGg -3' miRNA:   3'- -GGCGACAGCUAGGCCUCCGCGGCUCC- -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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