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
3625	5'	-42.7	NC_001650.1	+	154688	0.66	1
	Target:  5'- ----cUUCAGGUGCCUGAugGCccugGUCAa -3' miRNA:   3'- gucuuAAGUUCACGGAUU--UGa---UAGUc -5'
3625	5'	-42.7	NC_001650.1	+	115206	0.66	1
	Target:  5'- cCAGGugcgUCAGGcucUGCCUGAACgagauccUGUCGGu -3' miRNA:   3'- -GUCUua--AGUUC---ACGGAUUUG-------AUAGUC- -5'
3625	5'	-42.7	NC_001650.1	+	91976	0.67	1
	Target:  5'- aCGGucUUCAAGUGCCUGAcCaacCAGa -3' miRNA:   3'- -GUCuuAAGUUCACGGAUUuGauaGUC- -5'
3625	5'	-42.7	NC_001650.1	+	59373	0.67	1
	Target:  5'- aCAGAA-UCAGGUGCauaaacCUGAGCUGcgCGGc -3' miRNA:   3'- -GUCUUaAGUUCACG------GAUUUGAUa-GUC- -5'
3625	5'	-42.7	NC_001650.1	+	37422	0.66	1
	Target:  5'- aAGAccUUCAAGUGCCUGAucuuACUGa--- -3' miRNA:   3'- gUCUu-AAGUUCACGGAUU----UGAUaguc -5'
3625	5'	-42.7	NC_001650.1	+	143932	0.66	1
	Target:  5'- cCGGg---CAGGUGCCUGGuGCUGUCc- -3' miRNA:   3'- -GUCuuaaGUUCACGGAUU-UGAUAGuc -5'
3625	5'	-42.7	NC_001650.1	+	19124	0.67	1
	Target:  5'- aAGGAUgaAAGUGUCUGuucuGACUAUCAc -3' miRNA:   3'- gUCUUAagUUCACGGAU----UUGAUAGUc -5'
3625	5'	-42.7	NC_001650.1	+	38535	0.68	1
	Target:  5'- -uGAAa--AGGUGCUUAAACUAUCGc -3' miRNA:   3'- guCUUaagUUCACGGAUUUGAUAGUc -5'
3625	5'	-42.7	NC_001650.1	+	38411	0.69	0.999996
	Target:  5'- ---cAUUC-AGUGCUUAAACUGUCGc -3' miRNA:   3'- gucuUAAGuUCACGGAUUUGAUAGUc -5'
3625	5'	-42.7	NC_001650.1	+	126401	0.7	0.999989
	Target:  5'- aUAGGAUcgGAGUGUCUGAGCcguUCAGa -3' miRNA:   3'- -GUCUUAagUUCACGGAUUUGau-AGUC- -5'
3625	5'	-42.7	NC_001650.1	+	38710	1.1	0.057401
	Target:  5'- gCAGAAUUCAAGUGCCUAAACUAUCAGu -3' miRNA:   3'- -GUCUUAAGUUCACGGAUUUGAUAGUC- -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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