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
30610	5'	-55.3	NC_006549.1	+	40941	0.66	0.895509
	Target:  5'- -cACGGGCCccccggGCCCgauGGGGCCGa-- -3' miRNA:   3'- uuUGCCCGGa-----UGGGau-UUUCGGCggu -5'
30610	5'	-55.3	NC_006549.1	+	50248	0.67	0.853992
	Target:  5'- cAGGCGGGCCagcgucucccacggGCCCUu--GGaCGCCAg -3' miRNA:   3'- -UUUGCCCGGa-------------UGGGAuuuUCgGCGGU- -5'
30610	5'	-55.3	NC_006549.1	+	50991	0.67	0.842527
	Target:  5'- ---aGGGCCgaucgGCCCUAAGGGgC-CCAu -3' miRNA:   3'- uuugCCCGGa----UGGGAUUUUCgGcGGU- -5'
30610	5'	-55.3	NC_006549.1	+	41849	0.69	0.740537
	Target:  5'- uAGCGGGCCcgcgaggACCCccGGGGgCGCCGg -3' miRNA:   3'- uUUGCCCGGa------UGGGauUUUCgGCGGU- -5'
30610	5'	-55.3	NC_006549.1	+	3581	0.71	0.6475
	Target:  5'- -cGCGGGCCU-CgCUAAGGGUauaGCCAu -3' miRNA:   3'- uuUGCCCGGAuGgGAUUUUCGg--CGGU- -5'
30610	5'	-55.3	NC_006549.1	+	53451	0.71	0.626441
	Target:  5'- cGAGCGGGCg-GCCgaAgagauugcgGAAGCCGCCAu -3' miRNA:   3'- -UUUGCCCGgaUGGgaU---------UUUCGGCGGU- -5'
30610	5'	-55.3	NC_006549.1	+	83462	0.95	0.022886
	Target:  5'- aAAACGGGCUcACCCUAAAAGCCGCCAu -3' miRNA:   3'- -UUUGCCCGGaUGGGAUUUUCGGCGGU- -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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