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
2527	3'	-53.4	NC_001454.1	+	6733	0.66	0.70101
	Target:  5'- aCCCAGCAUguaaaacucgUUUACgGCCUuguaUGGgCAGc -3' miRNA:   3'- -GGGUUGUGa---------AAGUGgCGGA----ACCgGUC- -5'
2527	3'	-53.4	NC_001454.1	+	9596	0.66	0.66674
	Target:  5'- gCCgAACGCguagUUGCCGaCUUGGCCc- -3' miRNA:   3'- -GGgUUGUGaa--AGUGGCgGAACCGGuc -5'
2527	3'	-53.4	NC_001454.1	+	15612	0.67	0.632147
	Target:  5'- cCCCGcCACUgcaccCGCCGCCggggGGCaaaGGa -3' miRNA:   3'- -GGGUuGUGAaa---GUGGCGGaa--CCGg--UC- -5'
2527	3'	-53.4	NC_001454.1	+	11379	0.67	0.597551
	Target:  5'- gCCAACAUaaccaGCCGCCUccagGGcCCGGg -3' miRNA:   3'- gGGUUGUGaaag-UGGCGGAa---CC-GGUC- -5'
2527	3'	-53.4	NC_001454.1	+	17377	0.69	0.496496
	Target:  5'- cUCCGACGCUUggCACCGCCguuucucGCCc- -3' miRNA:   3'- -GGGUUGUGAAa-GUGGCGGaac----CGGuc -5'
2527	3'	-53.4	NC_001454.1	+	15970	0.71	0.37549
	Target:  5'- cUCCAACaccuccucaaGCUUUUGCCGCUUUGGCa-- -3' miRNA:   3'- -GGGUUG----------UGAAAGUGGCGGAACCGguc -5'
2527	3'	-53.4	NC_001454.1	+	31979	1.1	0.000731
	Target:  5'- uCCCAACACUUUCACCGCCUUGGCCAGc -3' miRNA:   3'- -GGGUUGUGAAAGUGGCGGAACCGGUC- -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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