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
33321	5'	-49.3	NC_007605.1	+	60626	0.66	0.998622
	Target:  5'- cCUCUGgcgacggaagaGGAGGAGgaGGCGGUGgUa-- -3' miRNA:   3'- -GAGAC-----------UCUUCUCgaCUGCCAUgAaua -5'
33321	5'	-49.3	NC_007605.1	+	90488	0.67	0.993652
	Target:  5'- -aCUGGGAAcAGCUGA-GGUGCUg-- -3' miRNA:   3'- gaGACUCUUcUCGACUgCCAUGAaua -5'
33321	5'	-49.3	NC_007605.1	+	133605	0.68	0.992653
	Target:  5'- -gCUGAugacaGAAGuGgUGGCGGUGCUUGa -3' miRNA:   3'- gaGACU-----CUUCuCgACUGCCAUGAAUa -5'
33321	5'	-49.3	NC_007605.1	+	5119	0.68	0.988889
	Target:  5'- -cCUuGGggGAGCUGGgGGUGCa--- -3' miRNA:   3'- gaGAcUCuuCUCGACUgCCAUGaaua -5'
33321	5'	-49.3	NC_007605.1	+	51030	0.7	0.961599
	Target:  5'- -cUUGAGggGGGCUGuugUGGUGCUg-- -3' miRNA:   3'- gaGACUCuuCUCGACu--GCCAUGAaua -5'
33321	5'	-49.3	NC_007605.1	+	11039	0.71	0.949475
	Target:  5'- aUCUGGGAGGAGC-GACGGa--UUAUa -3' miRNA:   3'- gAGACUCUUCUCGaCUGCCaugAAUA- -5'
33321	5'	-49.3	NC_007605.1	+	5938	0.74	0.862
	Target:  5'- uUCUGAGGAGGGCUGGgccCGGgGCUa-- -3' miRNA:   3'- gAGACUCUUCUCGACU---GCCaUGAaua -5'
33321	5'	-49.3	NC_007605.1	+	66648	1.07	0.016057
	Target:  5'- cCUCUGAGAAGAGCUGACGGUACUUAUa -3' miRNA:   3'- -GAGACUCUUCUCGACUGCCAUGAAUA- -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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