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
693	3'	-52	AC_000018.1	+	27646	0.66	0.733354
	Target:  5'- --cCACUGCCGccGCuuUCGCUGCuucGCc -3' miRNA:   3'- guaGUGACGGU--UGu-AGCGACGuu-CGc -5'
693	3'	-52	AC_000018.1	+	28865	0.66	0.755677
	Target:  5'- aAUUAUUGCCAACAuugucacugUCGCUcaCGGGCa -3' miRNA:   3'- gUAGUGACGGUUGU---------AGCGAc-GUUCGc -5'
693	3'	-52	AC_000018.1	+	17900	0.66	0.755677
	Target:  5'- -cUCG-UGCCGAUGUCGCUcCAGGUGc -3' miRNA:   3'- guAGUgACGGUUGUAGCGAcGUUCGC- -5'
693	3'	-52	AC_000018.1	+	5897	0.67	0.65229
	Target:  5'- -cUCACUGUCuuccGgAUCGCUGUccagGAGCGc -3' miRNA:   3'- guAGUGACGGu---UgUAGCGACG----UUCGC- -5'
693	3'	-52	AC_000018.1	+	33226	0.67	0.699033
	Target:  5'- --aCACUGCCAACAcCGCucccccagccaUGCAuugaAGUGa -3' miRNA:   3'- guaGUGACGGUUGUaGCG-----------ACGU----UCGC- -5'
693	3'	-52	AC_000018.1	+	12167	0.69	0.547004
	Target:  5'- aGUCGCaggGCCAugGagGCUGCAGGg- -3' miRNA:   3'- gUAGUGa--CGGUugUagCGACGUUCgc -5'
693	3'	-52	AC_000018.1	+	1037	0.7	0.524194
	Target:  5'- uGUCcggaGCUGCCugGACAUgGCUGUAAGUc -3' miRNA:   3'- gUAG----UGACGG--UUGUAgCGACGUUCGc -5'
693	3'	-52	AC_000018.1	+	23798	1.08	0.001151
	Target:  5'- cCAUCACUGCCAACAUCGCUGCAAGCGc -3' miRNA:   3'- -GUAGUGACGGUUGUAGCGACGUUCGC- -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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