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
16972	5'	-59	NC_004323.1	+	106329	0.66	0.790538
	Target:  5'- uGGUGUGUGCCGgCGGau-UGGUGCa -3' miRNA:   3'- cCCAUGCACGGCgGCCgcuGCCAUGg -5'
16972	5'	-59	NC_004323.1	+	66423	0.66	0.781636
	Target:  5'- ----cCGUGCCGCCGuGCGACaacaaGUcuGCCg -3' miRNA:   3'- cccauGCACGGCGGC-CGCUGc----CA--UGG- -5'
16972	5'	-59	NC_004323.1	+	109451	0.66	0.768049
	Target:  5'- uGGUACGcucaacaauuugcugGCCGCUaucgaaaacuugauaGGCGGCGGUGg- -3' miRNA:   3'- cCCAUGCa--------------CGGCGG---------------CCGCUGCCAUgg -5'
16972	5'	-59	NC_004323.1	+	44122	0.67	0.763462
	Target:  5'- cGGGUAaaGUGCUGCgaucuuaauuaCGGCGGCGucccGCCg -3' miRNA:   3'- -CCCAUg-CACGGCG-----------GCCGCUGCca--UGG- -5'
16972	5'	-59	NC_004323.1	+	53837	0.68	0.687051
	Target:  5'- cGGGcACG-GgCGCCGGCGGCuGUGg- -3' miRNA:   3'- -CCCaUGCaCgGCGGCCGCUGcCAUgg -5'
16972	5'	-59	NC_004323.1	+	64795	0.74	0.35579
	Target:  5'- aGGUACc-GUCGCCGGCGGCacGUACCc -3' miRNA:   3'- cCCAUGcaCGGCGGCCGCUGc-CAUGG- -5'
16972	5'	-59	NC_004323.1	+	64952	1.13	0.000862
	Target:  5'- cGGGUACGUGCCGCCGGCGACGGUACCu -3' miRNA:   3'- -CCCAUGCACGGCGGCCGCUGCCAUGG- -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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