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
11705	3'	-51.5	NC_003102.1	+	79679	0.66	0.990698
	Target:  5'- gCGAGACCGGaUCGAUUGAuacCAa-- -3' miRNA:   3'- -GCUCUGGCCaAGCUAGCUucuGUcua -5'
11705	3'	-51.5	NC_003102.1	+	1752	0.66	0.990698
	Target:  5'- -aGGAUCgauGGUUCGAUCGGuuuAGACAGu- -3' miRNA:   3'- gcUCUGG---CCAAGCUAGCU---UCUGUCua -5'
11705	3'	-51.5	NC_003102.1	+	1818	0.66	0.990698
	Target:  5'- -aGGAUCgauGGUUCGAUCGGuuuAGACAGu- -3' miRNA:   3'- gcUCUGG---CCAAGCUAGCU---UCUGUCua -5'
11705	3'	-51.5	NC_003102.1	+	114804	0.66	0.986317
	Target:  5'- uGuGACCGaUUCGAUCGAgucuauAGACAcGAUc -3' miRNA:   3'- gCuCUGGCcAAGCUAGCU------UCUGU-CUA- -5'
11705	3'	-51.5	NC_003102.1	+	22112	0.68	0.96008
	Target:  5'- --cGGCCGGUUUGGUgCGAAGAUAa-- -3' miRNA:   3'- gcuCUGGCCAAGCUA-GCUUCUGUcua -5'
11705	3'	-51.5	NC_003102.1	+	136452	0.68	0.956271
	Target:  5'- cCGua--CGGUUCGAaUGAAGGCAGAUg -3' miRNA:   3'- -GCucugGCCAAGCUaGCUUCUGUCUA- -5'
11705	3'	-51.5	NC_003102.1	+	64559	0.76	0.639014
	Target:  5'- aGGGACCGGcucgagaUUUGAUCGAcggAGACGGAg -3' miRNA:   3'- gCUCUGGCC-------AAGCUAGCU---UCUGUCUa -5'
11705	3'	-51.5	NC_003102.1	+	136799	1.06	0.01122
	Target:  5'- aCGAGACCGGUUCGAUCGAAGACAGAUc -3' miRNA:   3'- -GCUCUGGCCAAGCUAGCUUCUGUCUA- -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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