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
2245	5'	-60.9	NC_001405.1	+	17653	0.66	0.307577
	Target:  5'- --gGGUGGUaGCGCgcuGUUGGcaGCACCAg -3' miRNA:   3'- cugCCACCA-CGCGag-CAGCC--CGUGGU- -5'
2245	5'	-60.9	NC_001405.1	+	26930	0.66	0.292715
	Target:  5'- cGCGGgucgauacGgGUUCGUUGGGCGCCAg -3' miRNA:   3'- cUGCCacca----CgCGAGCAGCCCGUGGU- -5'
2245	5'	-60.9	NC_001405.1	+	13954	0.69	0.209607
	Target:  5'- cGACgGGUGGgcggGCGCggGcCGGGCACa- -3' miRNA:   3'- -CUG-CCACCa---CGCGagCaGCCCGUGgu -5'
2245	5'	-60.9	NC_001405.1	+	15719	0.7	0.173864
	Target:  5'- uGACGGUGGUGaugguggggGCUgG-CGGGCgcGCCAa -3' miRNA:   3'- -CUGCCACCACg--------CGAgCaGCCCG--UGGU- -5'
2245	5'	-60.9	NC_001405.1	+	5323	0.71	0.143656
	Target:  5'- cACGGUgaaggGGUGCGCUC--CGGGCugCGc -3' miRNA:   3'- cUGCCA-----CCACGCGAGcaGCCCGugGU- -5'
2245	5'	-60.9	NC_001405.1	+	16063	0.71	0.143656
	Target:  5'- cGACGGUGGUGCGCccaGUgCGGccgcguuugugcGCGCCc -3' miRNA:   3'- -CUGCCACCACGCGag-CA-GCC------------CGUGGu -5'
2245	5'	-60.9	NC_001405.1	+	6371	1.08	0.000192
	Target:  5'- aGACGGUGGUGCGCUCGUCGGGCACCAg -3' miRNA:   3'- -CUGCCACCACGCGAGCAGCCCGUGGU- -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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