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
2090	5'	-54.7	NC_001348.1	+	123537	0.67	0.860224
	Target:  5'- aUCAcGUGUACguccgGGCCCCgGCGcGaCCGg -3' miRNA:   3'- -AGUuUACGUGaa---CCGGGG-CGUaC-GGC- -5'
2090	5'	-54.7	NC_001348.1	+	106255	0.67	0.860224
	Target:  5'- aUCAcGUGUACguccgGGCCCCgGCGcGaCCGg -3' miRNA:   3'- -AGUuUACGUGaa---CCGGGG-CGUaC-GGC- -5'
2090	5'	-54.7	NC_001348.1	+	119051	0.68	0.80914
	Target:  5'- aCAAAacGCGCcggGGCCCCGCGacguaucccgGCCGu -3' miRNA:   3'- aGUUUa-CGUGaa-CCGGGGCGUa---------CGGC- -5'
2090	5'	-54.7	NC_001348.1	+	110741	0.68	0.80914
	Target:  5'- aCAAAacGCGCcggGGCCCCGCGacguaucccgGCCGu -3' miRNA:   3'- aGUUUa-CGUGaa-CCGGGGCGUa---------CGGC- -5'
2090	5'	-54.7	NC_001348.1	+	50832	0.69	0.778302
	Target:  5'- --cAGUGCccACggGGCCCCuggguuacguuuauGCGUGCCGg -3' miRNA:   3'- aguUUACG--UGaaCCGGGG--------------CGUACGGC- -5'
2090	5'	-54.7	NC_001348.1	+	87089	0.69	0.761801
	Target:  5'- aCGAAcacUGCGCgcguaGGCCCCGCAaGgCGa -3' miRNA:   3'- aGUUU---ACGUGaa---CCGGGGCGUaCgGC- -5'
2090	5'	-54.7	NC_001348.1	+	90186	1.1	0.002237
	Target:  5'- aUCAAAUGCACUUGGCCCCGCAUGCCGa -3' miRNA:   3'- -AGUUUACGUGAACCGGGGCGUACGGC- -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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