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
660	3'	-46	AC_000017.1	+	10363	0.66	0.989521
	Target:  5'- -cUGGCgGUAGAGGGGCcagcguagGGUgGCCGg -3' miRNA:   3'- gcACUGgCAUUUUUUUGa-------CCAgUGGC- -5'
660	3'	-46	AC_000017.1	+	4184	0.66	0.989521
	Target:  5'- --cGACCG-AGAcc-GCUGGUC-CCGg -3' miRNA:   3'- gcaCUGGCaUUUuuuUGACCAGuGGC- -5'
660	3'	-46	AC_000017.1	+	18794	0.66	0.987869
	Target:  5'- aUGUcGCCGccAGAGGAGCUGcugaGUCGCCGc -3' miRNA:   3'- -GCAcUGGCa-UUUUUUUGAC----CAGUGGC- -5'
660	3'	-46	AC_000017.1	+	1437	0.66	0.981692
	Target:  5'- aGUuGCCGUGAGAGuuGgUGGgcgUCGCCGg -3' miRNA:   3'- gCAcUGGCAUUUUUu-UgACC---AGUGGC- -5'
660	3'	-46	AC_000017.1	+	20850	0.66	0.981692
	Target:  5'- gGUagUCGUuAAAGGACUGGUCGuuGg -3' miRNA:   3'- gCAcuGGCAuUUUUUUGACCAGUggC- -5'
660	3'	-46	AC_000017.1	+	35667	0.68	0.96656
	Target:  5'- uGUGACUGauu--GAGCUGGU-GCCGu -3' miRNA:   3'- gCACUGGCauuuuUUUGACCAgUGGC- -5'
660	3'	-46	AC_000017.1	+	17110	0.68	0.949312
	Target:  5'- -aUGACCGUGGAGccuGGGCUGGagC-CCGa -3' miRNA:   3'- gcACUGGCAUUUU---UUUGACCa-GuGGC- -5'
660	3'	-46	AC_000017.1	+	35246	1.1	0.005461
	Target:  5'- gCGUGACCGUAAAAAAACUGGUCACCGu -3' miRNA:   3'- -GCACUGGCAUUUUUUUGACCAGUGGC- -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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