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
629	3'	-57.3	AC_000017.1	+	9855	0.66	0.51714
	Target:  5'- aUGUCCUUGGGUccGGccUGCUgaaugcgcagGCGGUCg -3' miRNA:   3'- -ACAGGAGCUCG--CCaaACGG----------CGCCAGg -5'
629	3'	-57.3	AC_000017.1	+	16338	0.68	0.366856
	Target:  5'- gGUCCaggcgaCGAGCGGccgccgcagcaGCCGCGG-CCa -3' miRNA:   3'- aCAGGa-----GCUCGCCaaa--------CGGCGCCaGG- -5'
629	3'	-57.3	AC_000017.1	+	15186	0.69	0.353044
	Target:  5'- aUGUCCUCcacCGGcugcaUUGCCGCGGcugCCg -3' miRNA:   3'- -ACAGGAGcucGCCa----AACGGCGCCa--GG- -5'
629	3'	-57.3	AC_000017.1	+	30716	0.7	0.297019
	Target:  5'- uUGUagCUaaGGCGGUggUUGCUGUGGUCCu -3' miRNA:   3'- -ACAg-GAgcUCGCCA--AACGGCGCCAGG- -5'
629	3'	-57.3	AC_000017.1	+	8536	0.75	0.14428
	Target:  5'- gGUaCCgcgcggCGGGCGGUggGCCGCGGgggugUCCu -3' miRNA:   3'- aCA-GGa-----GCUCGCCAaaCGGCGCC-----AGG- -5'
629	3'	-57.3	AC_000017.1	+	17271	0.76	0.115154
	Target:  5'- cG-CCUCG-GCGGUggcagaUGCCGCGGUgCa -3' miRNA:   3'- aCaGGAGCuCGCCAa-----ACGGCGCCAgG- -5'
629	3'	-57.3	AC_000017.1	+	5789	0.96	0.00401
	Target:  5'- cUGUCCUCGAGCGGUguuCCGCGGUCCu -3' miRNA:   3'- -ACAGGAGCUCGCCAaacGGCGCCAGG- -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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