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
265	5'	-55.5	AC_000008.1	+	10544	0.66	0.604367
	Target:  5'- ---gCUCuGGCCGGUcaGGCGCgCGCAAUc -3' miRNA:   3'- ggaaGAG-CCGGCCG--UUGCG-GUGUUGu -5'
265	5'	-55.5	AC_000008.1	+	26697	0.66	0.604367
	Target:  5'- aCCgg--CGGCagCGGCAGCGgCAgCAACAg -3' miRNA:   3'- -GGaagaGCCG--GCCGUUGCgGU-GUUGU- -5'
265	5'	-55.5	AC_000008.1	+	23859	0.66	0.593109
	Target:  5'- gCUgagCUCGcgccGCCGGCucACGCuCACGGCc -3' miRNA:   3'- gGAa--GAGC----CGGCCGu-UGCG-GUGUUGu -5'
265	5'	-55.5	AC_000008.1	+	12205	0.66	0.581886
	Target:  5'- cCCgcg-CGcGCUGGCAACGUCgGCGGCGu -3' miRNA:   3'- -GGaagaGC-CGGCCGUUGCGG-UGUUGU- -5'
265	5'	-55.5	AC_000008.1	+	3093	0.67	0.515768
	Target:  5'- aCCUgCUCGGaCGGCAACuGUCACcuGCu -3' miRNA:   3'- -GGAaGAGCCgGCCGUUG-CGGUGu-UGu -5'
265	5'	-55.5	AC_000008.1	+	18426	0.7	0.358249
	Target:  5'- gUCUUCUgGGgCGGUAGguguaGCCACGAUAg -3' miRNA:   3'- -GGAAGAgCCgGCCGUUg----CGGUGUUGU- -5'
265	5'	-55.5	AC_000008.1	+	19616	0.74	0.213309
	Target:  5'- gCCUUCgagCGGCCcGCAugGCCGCc--- -3' miRNA:   3'- -GGAAGa--GCCGGcCGUugCGGUGuugu -5'
265	5'	-55.5	AC_000008.1	+	21650	1.1	0.000455
	Target:  5'- cCCUUCUCGGCCGGCAACGCCACAACAu -3' miRNA:   3'- -GGAAGAGCCGGCCGUUGCGGUGUUGU- -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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