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
21049	5'	-55.2	NC_004745.1	+	20765	0.66	0.511156
	Target:  5'- -gCGGCAGcaUCAGCGcgcagcCAGUGCCUGc -3' miRNA:   3'- aaGUCGUCc-AGUCGUa-----GUCACGGACc -5'
21049	5'	-55.2	NC_004745.1	+	21673	0.66	0.489067
	Target:  5'- aUCAGCAuGUaaucCGGCGUCAGcguacUGCCUGc -3' miRNA:   3'- aAGUCGUcCA----GUCGUAGUC-----ACGGACc -5'
21049	5'	-55.2	NC_004745.1	+	10826	0.66	0.485791
	Target:  5'- gUCGGUGGGUgccuaucaguaucaUGGCcgCAGUGCCgacGGg -3' miRNA:   3'- aAGUCGUCCA--------------GUCGuaGUCACGGa--CC- -5'
21049	5'	-55.2	NC_004745.1	+	389	0.66	0.467434
	Target:  5'- -cCAGCAGGUCAGCg-----GCgCUGGc -3' miRNA:   3'- aaGUCGUCCAGUCGuagucaCG-GACC- -5'
21049	5'	-55.2	NC_004745.1	+	8823	0.67	0.445262
	Target:  5'- -cCAGCGuucgcucGGUCAGCAUCAG-GCUg-- -3' miRNA:   3'- aaGUCGU-------CCAGUCGUAGUCaCGGacc -5'
21049	5'	-55.2	NC_004745.1	+	18459	0.76	0.11319
	Target:  5'- -gCGGCGaccuccugcucGGUCAGCAUCGGUGCCg-- -3' miRNA:   3'- aaGUCGU-----------CCAGUCGUAGUCACGGacc -5'
21049	5'	-55.2	NC_004745.1	+	17252	1.07	0.000469
	Target:  5'- gUUCAGCAGGUCAGCAUCAGUGCCUGGc -3' miRNA:   3'- -AAGUCGUCCAGUCGUAGUCACGGACC- -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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