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
27924	3'	-52	NC_005886.2	+	26676	0.66	0.836395
	Target:  5'- uGUUGCCGUCCGAUucGAgcgugACGGcgaACAu -3' miRNA:   3'- cUAGCGGCAGGCUA--CUa----UGCCa--UGUu -5'
27924	3'	-52	NC_005886.2	+	18021	0.66	0.836395
	Target:  5'- ---aGCCGUCCGGUGAUAagcCGGc---- -3' miRNA:   3'- cuagCGGCAGGCUACUAU---GCCauguu -5'
27924	3'	-52	NC_005886.2	+	42455	0.68	0.734537
	Target:  5'- --cCGCCGcacUCCGGgugGAUgcGCGGUGCGg -3' miRNA:   3'- cuaGCGGC---AGGCUa--CUA--UGCCAUGUu -5'
27924	3'	-52	NC_005886.2	+	37349	0.7	0.621549
	Target:  5'- ---aGcCCGUCCGGUGAgACGaGUACGAa -3' miRNA:   3'- cuagC-GGCAGGCUACUaUGC-CAUGUU- -5'
27924	3'	-52	NC_005886.2	+	40723	0.72	0.498457
	Target:  5'- -cUCGCUGUUCGAgcgGAUGCGG-ACGGg -3' miRNA:   3'- cuAGCGGCAGGCUa--CUAUGCCaUGUU- -5'
27924	3'	-52	NC_005886.2	+	29284	0.72	0.498457
	Target:  5'- --gCGCCGUUCGAUGAagccgcUGCGcGUGCGGg -3' miRNA:   3'- cuaGCGGCAGGCUACU------AUGC-CAUGUU- -5'
27924	3'	-52	NC_005886.2	+	10124	0.74	0.406393
	Target:  5'- --cCGUgGUuuGGUGAUACGGUGCGc -3' miRNA:   3'- cuaGCGgCAggCUACUAUGCCAUGUu -5'
27924	3'	-52	NC_005886.2	+	13227	1.06	0.002629
	Target:  5'- gGAUCGCCGUCCGAUGAUACGGUACAAg -3' miRNA:   3'- -CUAGCGGCAGGCUACUAUGCCAUGUU- -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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