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
9631	3'	-58.6	NC_002577.1	+	161199	0.66	0.762789
	Target:  5'- -cCCaggCGGCGCUCUCCGGUagGCagagGCGGu -3' miRNA:   3'- aaGGa--GCCGCGAGAGGUUA--CGg---CGUU- -5'
9631	3'	-58.6	NC_002577.1	+	136139	0.66	0.762789
	Target:  5'- -cCCaggCGGCGCUCUCCGGUagGCagagGCGGu -3' miRNA:   3'- aaGGa--GCCGCGAGAGGUUA--CGg---CGUU- -5'
9631	3'	-58.6	NC_002577.1	+	10551	0.66	0.733671
	Target:  5'- -cCCUugCGGCGCUCUacgaaagaacCCGAUgagGCCGCGu -3' miRNA:   3'- aaGGA--GCCGCGAGA----------GGUUA---CGGCGUu -5'
9631	3'	-58.6	NC_002577.1	+	123063	0.66	0.733671
	Target:  5'- -cCCUugCGGCGCUCUacgaaagaacCCGAUgagGCCGCGu -3' miRNA:   3'- aaGGA--GCCGCGAGA----------GGUUA---CGGCGUu -5'
9631	3'	-58.6	NC_002577.1	+	139190	0.69	0.601394
	Target:  5'- -cCCUCccGCGCUUUCCGcgGCCGuCAGg -3' miRNA:   3'- aaGGAGc-CGCGAGAGGUuaCGGC-GUU- -5'
9631	3'	-58.6	NC_002577.1	+	158148	0.69	0.601394
	Target:  5'- -cCCUCccGCGCUUUCCGcgGCCGuCAGg -3' miRNA:   3'- aaGGAGc-CGCGAGAGGUuaCGGC-GUU- -5'
9631	3'	-58.6	NC_002577.1	+	115805	1.03	0.003234
	Target:  5'- uUUCCUCGGCGCUCUCCAAUGCCGCAAc -3' miRNA:   3'- -AAGGAGCCGCGAGAGGUUACGGCGUU- -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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