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
2739	5'	-53.8	NC_001491.2	+	121541	0.66	0.958803
	Target:  5'- uCGAUGCGCUGGCUggagCGUggggacGGGUCCc-- -3' miRNA:   3'- -GCUAUGCGGCUGGa---GCG------UCUAGGuau -5'
2739	5'	-53.8	NC_001491.2	+	145508	0.66	0.958803
	Target:  5'- --cUugGCCagauuGGCCUCGCGGAcgcccUCCAg- -3' miRNA:   3'- gcuAugCGG-----CUGGAGCGUCU-----AGGUau -5'
2739	5'	-53.8	NC_001491.2	+	9494	0.66	0.950896
	Target:  5'- aGGUACGUCGACCUUcgaauucagGCGGAcguggCCGa- -3' miRNA:   3'- gCUAUGCGGCUGGAG---------CGUCUa----GGUau -5'
2739	5'	-53.8	NC_001491.2	+	35839	0.66	0.950896
	Target:  5'- gGGUcacaACGUCGGCC-CGCAGGUCgGc- -3' miRNA:   3'- gCUA----UGCGGCUGGaGCGUCUAGgUau -5'
2739	5'	-53.8	NC_001491.2	+	139987	0.68	0.9138
	Target:  5'- cCGcUGCGCCGcgccguggggcgguACCUCGUGGAUCUcgGc -3' miRNA:   3'- -GCuAUGCGGC--------------UGGAGCGUCUAGGuaU- -5'
2739	5'	-53.8	NC_001491.2	+	54985	0.69	0.8528
	Target:  5'- gGAgguUGCUGGCCUCGCAGgAUUCGg- -3' miRNA:   3'- gCUau-GCGGCUGGAGCGUC-UAGGUau -5'
2739	5'	-53.8	NC_001491.2	+	131356	0.75	0.559322
	Target:  5'- cCGAUGCGCUGACCUCaCAGAgauagUCCu-- -3' miRNA:   3'- -GCUAUGCGGCUGGAGcGUCU-----AGGuau -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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