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
28529	5'	-49.3	NC_005946.1	+	94069	0.65	0.994921
	Target:  5'- uCCCAaggccuuuggagAGUCUGCUGUCAUcaggaccagcaggGgGAGGAGg -3' miRNA:   3'- -GGGU------------UCAGAUGACGGUGa------------CgCUUUUC- -5'
28529	5'	-49.3	NC_005946.1	+	68461	0.66	0.994421
	Target:  5'- uCCUGA-UCUGCUGCCcCUGgGuAAAGa -3' miRNA:   3'- -GGGUUcAGAUGACGGuGACgCuUUUC- -5'
28529	5'	-49.3	NC_005946.1	+	27362	0.66	0.992462
	Target:  5'- aCCAGGUCUGggucUUGCCACcGCa----- -3' miRNA:   3'- gGGUUCAGAU----GACGGUGaCGcuuuuc -5'
28529	5'	-49.3	NC_005946.1	+	79483	0.66	0.992462
	Target:  5'- gCCGAG-CUGgUGCCAUuaaagUGCGucGAGg -3' miRNA:   3'- gGGUUCaGAUgACGGUG-----ACGCuuUUC- -5'
28529	5'	-49.3	NC_005946.1	+	27077	0.67	0.986925
	Target:  5'- aCCCAgaAGUCUGCUGCaCAg-GC-AAAAGc -3' miRNA:   3'- -GGGU--UCAGAUGACG-GUgaCGcUUUUC- -5'
28529	5'	-49.3	NC_005946.1	+	13543	0.67	0.983184
	Target:  5'- cCCCAAGacguUUGCCuACUGCGAGu-- -3' miRNA:   3'- -GGGUUCagauGACGG-UGACGCUUuuc -5'
28529	5'	-49.3	NC_005946.1	+	27039	0.7	0.932028
	Target:  5'- gCCAAGUCUGcCUGUCGuCgGCGAGGu- -3' miRNA:   3'- gGGUUCAGAU-GACGGU-GaCGCUUUuc -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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