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
20619	3'	-50.4	NC_004688.1	+	6001	0.66	0.974678
	Target:  5'- ---cGCGCgGCgauGAGAUCUUGGAu- -3' miRNA:   3'- guuaCGCGaCGac-UUCUAGAGCCUuu -5'
20619	3'	-50.4	NC_004688.1	+	93557	0.66	0.974678
	Target:  5'- uCGAUGCGgaUGCcGggGAUUgcgCGGAAc -3' miRNA:   3'- -GUUACGCg-ACGaCuuCUAGa--GCCUUu -5'
20619	3'	-50.4	NC_004688.1	+	33796	0.66	0.974678
	Target:  5'- cCGGUGuCGUUGCUGuuGAUUuccccgcagUCGGGAAa -3' miRNA:   3'- -GUUAC-GCGACGACuuCUAG---------AGCCUUU- -5'
20619	3'	-50.4	NC_004688.1	+	86673	0.67	0.953454
	Target:  5'- cCGGUGCcCgggGCcccgcccgUGggGAUCUCGGGAGg -3' miRNA:   3'- -GUUACGcGa--CG--------ACuuCUAGAGCCUUU- -5'
20619	3'	-50.4	NC_004688.1	+	87417	0.69	0.922647
	Target:  5'- aCGGUGCGauagcggGCUGAAGAUUcUGGAAc -3' miRNA:   3'- -GUUACGCga-----CGACUUCUAGaGCCUUu -5'
20619	3'	-50.4	NC_004688.1	+	11683	0.69	0.922048
	Target:  5'- aGGUGCGCgaGCUcaaccccgagccgGAGGAUCUCGcGAAc -3' miRNA:   3'- gUUACGCGa-CGA-------------CUUCUAGAGC-CUUu -5'
20619	3'	-50.4	NC_004688.1	+	22701	0.71	0.831682
	Target:  5'- --uUGUGgaGCUGGAGAUCUuccCGGGAu -3' miRNA:   3'- guuACGCgaCGACUUCUAGA---GCCUUu -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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