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
1255	3'	-49.2	NC_001317.1	+	2224	0.67	0.842381
	Target:  5'- aUUUCAGGcGUGUaacGGAugcCGcGUGCGGCCg -3' miRNA:   3'- gAAAGUCC-CAUA---CCUu--GC-CGUGUUGG- -5'
1255	3'	-49.2	NC_001317.1	+	13245	0.67	0.841433
	Target:  5'- --aUCgAGGGggcgcgAUGGGGCGGUuuguugaGCGACUg -3' miRNA:   3'- gaaAG-UCCCa-----UACCUUGCCG-------UGUUGG- -5'
1255	3'	-49.2	NC_001317.1	+	17596	0.69	0.701997
	Target:  5'- ---gCAGGcGgcUGaGAAUGGCGCGGCUa -3' miRNA:   3'- gaaaGUCC-CauAC-CUUGCCGUGUUGG- -5'
1255	3'	-49.2	NC_001317.1	+	14134	0.7	0.678393
	Target:  5'- --gUCAGGGc-UGGAugaugucUGGCACAACUa -3' miRNA:   3'- gaaAGUCCCauACCUu------GCCGUGUUGG- -5'
1255	3'	-49.2	NC_001317.1	+	30053	0.72	0.571131
	Target:  5'- aUUUCAGGGUAauuuuagcgguUGGGAUGGCucuUAucGCCc -3' miRNA:   3'- gAAAGUCCCAU-----------ACCUUGCCGu--GU--UGG- -5'
1255	3'	-49.2	NC_001317.1	+	8839	0.74	0.425784
	Target:  5'- --aUCGGGGUuauuucGGAgcuGCGGCACGGCg -3' miRNA:   3'- gaaAGUCCCAua----CCU---UGCCGUGUUGg -5'
1255	3'	-49.2	NC_001317.1	+	1489	1.12	0.001268
	Target:  5'- gCUUUCAGGGUAUGGAACGGCACAACCc -3' miRNA:   3'- -GAAAGUCCCAUACCUUGCCGUGUUGG- -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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