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
21281	5'	-51.2	NC_004778.3	+	63597	0.66	0.98417
	Target:  5'- cGCCCAGG-GCCa---GAAUUUgGCGACg -3' miRNA:   3'- -UGGGUCCaCGGccagCUUAAA-UGUUG- -5'
21281	5'	-51.2	NC_004778.3	+	57388	0.66	0.979973
	Target:  5'- uGCUCGucuucgcgGCCGGUCGAGUccACAGCu -3' miRNA:   3'- -UGGGUcca-----CGGCCAGCUUAaaUGUUG- -5'
21281	5'	-51.2	NC_004778.3	+	9100	0.67	0.974998
	Target:  5'- uACaCCGGGUGCaGGUUGAGUaguaaaagUUGCAc- -3' miRNA:   3'- -UG-GGUCCACGgCCAGCUUA--------AAUGUug -5'
21281	5'	-51.2	NC_004778.3	+	100246	0.68	0.95227
	Target:  5'- uCCCAaGUGCCGGUCacgggcccgGCAGCu -3' miRNA:   3'- uGGGUcCACGGCCAGcuuaaa---UGUUG- -5'
21281	5'	-51.2	NC_004778.3	+	39405	0.69	0.931121
	Target:  5'- gGCCC-GGUGCUGGcgaCGAAUUUG-AGCa -3' miRNA:   3'- -UGGGuCCACGGCCa--GCUUAAAUgUUG- -5'
21281	5'	-51.2	NC_004778.3	+	43867	0.73	0.765199
	Target:  5'- --aCAGGUGCCGGcUCGGgagAUUUACGAg -3' miRNA:   3'- uggGUCCACGGCC-AGCU---UAAAUGUUg -5'
21281	5'	-51.2	NC_004778.3	+	39140	0.76	0.58606
	Target:  5'- uUCCAGGUcGUCGGUgGAcgUUACGACc -3' miRNA:   3'- uGGGUCCA-CGGCCAgCUuaAAUGUUG- -5'
21281	5'	-51.2	NC_004778.3	+	16006	1.11	0.005157
	Target:  5'- cACCCAGGUGCCGGUCGAAUUUACAACg -3' miRNA:   3'- -UGGGUCCACGGCCAGCUUAAAUGUUG- -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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