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
28903	3'	-48.9	NC_006146.1	+	81736	0.66	0.998746
	Target:  5'- cGCUGUgagCUCUCCAUUccccUGCgcgUUGCAu -3' miRNA:   3'- -CGAUAa--GGGGGGUAA----ACGagaAACGU- -5'
28903	3'	-48.9	NC_006146.1	+	42697	0.68	0.994918
	Target:  5'- gGCUGgcagagCCCCCCAgcgcccGCUCgggcugGCAg -3' miRNA:   3'- -CGAUaa----GGGGGGUaaa---CGAGaaa---CGU- -5'
28903	3'	-48.9	NC_006146.1	+	5070	0.68	0.994078
	Target:  5'- uGCUGUgCCCCCUGg--GaCUCUUgUGCAu -3' miRNA:   3'- -CGAUAaGGGGGGUaaaC-GAGAA-ACGU- -5'
28903	3'	-48.9	NC_006146.1	+	166062	0.68	0.992063
	Target:  5'- cCUAUUCCCCuCCA--UGCUgCUggugUGCu -3' miRNA:   3'- cGAUAAGGGG-GGUaaACGA-GAa---ACGu -5'
28903	3'	-48.9	NC_006146.1	+	92967	0.69	0.986431
	Target:  5'- uGCUAUcugcucugccugUCCCgCCuucUGCUUUUUGCAu -3' miRNA:   3'- -CGAUA------------AGGGgGGuaaACGAGAAACGU- -5'
28903	3'	-48.9	NC_006146.1	+	96304	0.82	0.470982
	Target:  5'- uGCUGUUCCCCCCAgcca-UCUUUGCc -3' miRNA:   3'- -CGAUAAGGGGGGUaaacgAGAAACGu -5'
28903	3'	-48.9	NC_006146.1	+	22210	1.12	0.008945
	Target:  5'- gGCUAUUCCCCCCAUUUGCUCUUUGCAg -3' miRNA:   3'- -CGAUAAGGGGGGUAAACGAGAAACGU- -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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