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
31755	3'	-58.8	NC_006938.1	+	37926	0.66	0.558337
	Target:  5'- -aGCGG-GCGguG-GCCaGGGCGGuGGa -3' miRNA:   3'- ugUGCCaCGCguCaCGGaCCCGUU-CC- -5'
31755	3'	-58.8	NC_006938.1	+	3698	0.66	0.527101
	Target:  5'- aGCgACGGUGCGCGuucauCCUGGaCGAGGc -3' miRNA:   3'- -UG-UGCCACGCGUcac--GGACCcGUUCC- -5'
31755	3'	-58.8	NC_006938.1	+	58569	0.66	0.527101
	Target:  5'- cGCAuCGGUgggGCGCucguGgaugGCCUGGGCAcugucccccuGGGc -3' miRNA:   3'- -UGU-GCCA---CGCGu---Ca---CGGACCCGU----------UCC- -5'
31755	3'	-58.8	NC_006938.1	+	35385	0.67	0.466807
	Target:  5'- -gACGGgaGUGCuGUGUgUaGGGCAGGGg -3' miRNA:   3'- ugUGCCa-CGCGuCACGgA-CCCGUUCC- -5'
31755	3'	-58.8	NC_006938.1	+	13345	0.71	0.27528
	Target:  5'- -gGCGGUGUcgacaaagccaGcCGGUGCCUGGGCGGa- -3' miRNA:   3'- ugUGCCACG-----------C-GUCACGGACCCGUUcc -5'
31755	3'	-58.8	NC_006938.1	+	22069	0.79	0.085571
	Target:  5'- -aGCGGcUGCGCGGcgGCCUGGGCAAa- -3' miRNA:   3'- ugUGCC-ACGCGUCa-CGGACCCGUUcc -5'
31755	3'	-58.8	NC_006938.1	+	27858	0.98	0.00333
	Target:  5'- gACACGGUGCGCAGUGCCUGGGaCAGGa -3' miRNA:   3'- -UGUGCCACGCGUCACGGACCC-GUUCc -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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