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
27615	5'	-56.3	NC_005882.1	+	5774	0.66	0.494365
	Target:  5'- gCGGc--GGGGCCGaccuGCUGCaCGGUGuGCc -3' miRNA:   3'- -GCCaauUCCCGGC----CGACG-GUCACuUG- -5'
27615	5'	-56.3	NC_005882.1	+	12478	0.66	0.483773
	Target:  5'- gGGUUc-GGGCCGGgaGCguGcucaUGAACu -3' miRNA:   3'- gCCAAuuCCCGGCCgaCGguC----ACUUG- -5'
27615	5'	-56.3	NC_005882.1	+	6097	0.66	0.483773
	Target:  5'- uCGGacAAcGGCCGcaGCUcGCCGGUGGACu -3' miRNA:   3'- -GCCaaUUcCCGGC--CGA-CGGUCACUUG- -5'
27615	5'	-56.3	NC_005882.1	+	16973	0.67	0.462924
	Target:  5'- uGGacGAGcGGCC-GCUGCCGGUGucCg -3' miRNA:   3'- gCCaaUUC-CCGGcCGACGGUCACuuG- -5'
27615	5'	-56.3	NC_005882.1	+	324	0.68	0.422705
	Target:  5'- uCGGUccgcAGGGGUCGucguagaucccGCguccGCCAGUGGACa -3' miRNA:   3'- -GCCAa---UUCCCGGC-----------CGa---CGGUCACUUG- -5'
27615	5'	-56.3	NC_005882.1	+	19264	0.68	0.403398
	Target:  5'- aGGcccUUGAGGGCCGGCgGCUgcgcaccgAG-GAACc -3' miRNA:   3'- gCC---AAUUCCCGGCCGaCGG--------UCaCUUG- -5'
27615	5'	-56.3	NC_005882.1	+	30881	1.1	0.000333
	Target:  5'- gCGGUUAAGGGCCGGCUGCCAGUGAACg -3' miRNA:   3'- -GCCAAUUCCCGGCCGACGGUCACUUG- -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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