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
1011	3'	-51.6	NC_000924.1	+	28904	0.66	0.923938
	Target:  5'- ----aUCUUUUUCuuCCggCACCAGUCCa -3' miRNA:   3'- aguagAGAGAAAGugGG--GUGGUCAGG- -5'
1011	3'	-51.6	NC_000924.1	+	59003	0.67	0.890641
	Target:  5'- -aAUCUCUCUcaccacaGCCUCACCAucGUUCg -3' miRNA:   3'- agUAGAGAGAaag----UGGGGUGGU--CAGG- -5'
1011	3'	-51.6	NC_000924.1	+	5488	0.67	0.873023
	Target:  5'- -gGUCUCUCUcguuugcuucugcuUUCGCCgCCAUCAuuUCCa -3' miRNA:   3'- agUAGAGAGA--------------AAGUGG-GGUGGUc-AGG- -5'
1011	3'	-51.6	NC_000924.1	+	31603	0.68	0.804707
	Target:  5'- aUCAUCUggCUCgucugacaUCACCaCCAgaUCAGUCCg -3' miRNA:   3'- -AGUAGA--GAGaa------AGUGG-GGU--GGUCAGG- -5'
1011	3'	-51.6	NC_000924.1	+	16434	0.69	0.798859
	Target:  5'- cCAUCgacgacaagUCACCCCACgaAGUCCa -3' miRNA:   3'- aGUAGagagaa---AGUGGGGUGg-UCAGG- -5'
1011	3'	-51.6	NC_000924.1	+	42771	0.71	0.689401
	Target:  5'- gUCAUC-CUCcg-UACCCCGCCAGauUUCa -3' miRNA:   3'- -AGUAGaGAGaaaGUGGGGUGGUC--AGG- -5'
1011	3'	-51.6	NC_000924.1	+	27615	1.12	0.001701
	Target:  5'- uUCAUCUCUCUUUCACCCCACCAGUCCc -3' miRNA:   3'- -AGUAGAGAGAAAGUGGGGUGGUCAGG- -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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