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
2981	5'	-52.3	NC_001493.1	+	113149	0.66	0.977603
	Target:  5'- uCUCUGCG-GUGAucccagaggcauACCCGUUauucguauacgaAUCGAa- -3' miRNA:   3'- -GAGACGCuCACU------------UGGGCAG------------UAGCUag -5'
2981	5'	-52.3	NC_001493.1	+	8427	0.66	0.972319
	Target:  5'- -gCUGCGGcuGUGGACCCGggcaccccccCGUCGAc- -3' miRNA:   3'- gaGACGCU--CACUUGGGCa---------GUAGCUag -5'
2981	5'	-52.3	NC_001493.1	+	123981	0.66	0.972319
	Target:  5'- -gCUGCGGcuGUGGACCCGggcaccccccCGUCGAc- -3' miRNA:   3'- gaGACGCU--CACUUGGGCa---------GUAGCUag -5'
2981	5'	-52.3	NC_001493.1	+	66219	0.67	0.955295
	Target:  5'- gCUUUgGCGGGUGGaagcucuacgacGCCCGUCuauugagucgcUCGAUCg -3' miRNA:   3'- -GAGA-CGCUCACU------------UGGGCAGu----------AGCUAG- -5'
2981	5'	-52.3	NC_001493.1	+	42014	0.68	0.942236
	Target:  5'- uCUCcGCGGGUGAucaacugcuguGCCCGagugCGAUCa -3' miRNA:   3'- -GAGaCGCUCACU-----------UGGGCaguaGCUAG- -5'
2981	5'	-52.3	NC_001493.1	+	73081	0.69	0.921311
	Target:  5'- aCUCgUGCGGGcgGGcACCCGUgAUCGAc- -3' miRNA:   3'- -GAG-ACGCUCa-CU-UGGGCAgUAGCUag -5'
2981	5'	-52.3	NC_001493.1	+	99687	1.09	0.005788
	Target:  5'- gCUCUGCGAGUGAACCCGUCAUCGAUCc -3' miRNA:   3'- -GAGACGCUCACUUGGGCAGUAGCUAG- -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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