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
32266	3'	-48.1	NC_007022.1	+	3356	0.66	0.999742
	Target:  5'- uGGGAUcuucGAUGGUUGGCAUgaCAUCu -3' miRNA:   3'- gUCCUAu---UUGCCAGUCGUAgaGUAGu -5'
32266	3'	-48.1	NC_007022.1	+	74785	0.66	0.999482
	Target:  5'- uGGGAUGAAauCGGUgAGaUAUUUCAUCc -3' miRNA:   3'- gUCCUAUUU--GCCAgUC-GUAGAGUAGu -5'
32266	3'	-48.1	NC_007022.1	+	155069	0.67	0.99902
	Target:  5'- -uGGAUAuccGACGGUUGGUAUCg-GUCAc -3' miRNA:   3'- guCCUAU---UUGCCAGUCGUAGagUAGU- -5'
32266	3'	-48.1	NC_007022.1	+	160345	0.67	0.99902
	Target:  5'- cCAGGAccggccauAACGaaGUCAGCGuUCUCAUCc -3' miRNA:   3'- -GUCCUau------UUGC--CAGUCGU-AGAGUAGu -5'
32266	3'	-48.1	NC_007022.1	+	65891	0.68	0.996998
	Target:  5'- -cGGAgccaacuguUGAAggUGGUCAGCAUCUCAa-- -3' miRNA:   3'- guCCU---------AUUU--GCCAGUCGUAGAGUagu -5'
32266	3'	-48.1	NC_007022.1	+	4569	0.69	0.995819
	Target:  5'- aGGGGUAaauagaaccuuGACcauccgGGUCAGCAUC-CGUCAu -3' miRNA:   3'- gUCCUAU-----------UUG------CCAGUCGUAGaGUAGU- -5'
32266	3'	-48.1	NC_007022.1	+	144478	1.1	0.015753
	Target:  5'- cCAGGAUAAACGGUCAGCAUCUCAUCAa -3' miRNA:   3'- -GUCCUAUUUGCCAGUCGUAGAGUAGU- -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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