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
19577	5'	-56.6	NC_004686.1	+	151	0.66	0.616903
	Target:  5'- -aACCUCAGCCCGCCgacgaucccggaUCGucGUGGAa-- -3' miRNA:   3'- agUGGGGUCGGGCGG------------AGU--CACUUaua -5'
19577	5'	-56.6	NC_004686.1	+	33923	0.66	0.605849
	Target:  5'- gUCACCCCGGCCCaagucGCCgucgCAGc------ -3' miRNA:   3'- -AGUGGGGUCGGG-----CGGa---GUCacuuaua -5'
19577	5'	-56.6	NC_004686.1	+	37795	0.66	0.57286
	Target:  5'- aCGCCCCGGUCCGguacaCCUCGGaauuacGGAUGc -3' miRNA:   3'- aGUGGGGUCGGGC-----GGAGUCa-----CUUAUa -5'
19577	5'	-56.6	NC_004686.1	+	22154	0.67	0.518959
	Target:  5'- cCGCCCUGG-CCGCCguucgCGGUGAGc-- -3' miRNA:   3'- aGUGGGGUCgGGCGGa----GUCACUUaua -5'
19577	5'	-56.6	NC_004686.1	+	47429	0.68	0.508408
	Target:  5'- aUCugCUCAGCCCacGCCUCgacGGUGGc--- -3' miRNA:   3'- -AGugGGGUCGGG--CGGAG---UCACUuaua -5'
19577	5'	-56.6	NC_004686.1	+	37194	0.68	0.487587
	Target:  5'- -gGCagaCCAGucaCCCGUCUCGGUGggUGa -3' miRNA:   3'- agUGg--GGUC---GGGCGGAGUCACuuAUa -5'
19577	5'	-56.6	NC_004686.1	+	18046	0.7	0.390338
	Target:  5'- cCACCCguGgCCGUUUCAGUGAc--- -3' miRNA:   3'- aGUGGGguCgGGCGGAGUCACUuaua -5'
19577	5'	-56.6	NC_004686.1	+	13393	1.06	0.000945
	Target:  5'- cUCACCCCAGCCCGCCUCAGUGAAUAUg -3' miRNA:   3'- -AGUGGGGUCGGGCGGAGUCACUUAUA- -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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