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
22307	5'	-55.1	NC_005045.1	+	26725	0.66	0.693307
	Target:  5'- uGGGGGUGcAGuucauGGACGGCGcuGUCAuGGCc -3' miRNA:   3'- gCUCCCAU-UC-----CCUGCCGCc-UAGU-UCG- -5'
22307	5'	-55.1	NC_005045.1	+	37649	0.66	0.649026
	Target:  5'- -cAGGGUGcgcGGGAcCGGCGGGauaUCAacgaccgcAGCg -3' miRNA:   3'- gcUCCCAUu--CCCU-GCCGCCU---AGU--------UCG- -5'
22307	5'	-55.1	NC_005045.1	+	894	0.67	0.615608
	Target:  5'- gCGAGGGUAuugacacGuGGGCGGCaGGUCuguaGAGUu -3' miRNA:   3'- -GCUCCCAUu------C-CCUGCCGcCUAG----UUCG- -5'
22307	5'	-55.1	NC_005045.1	+	40393	0.68	0.518171
	Target:  5'- gCGAGGGUGccuuugcccgccucGG-UGGCGGuAUCGAGCa -3' miRNA:   3'- -GCUCCCAUuc------------CCuGCCGCC-UAGUUCG- -5'
22307	5'	-55.1	NC_005045.1	+	42137	0.75	0.217015
	Target:  5'- aCGGGGG-AAGGGugGGCGuGUCgGAGUc -3' miRNA:   3'- -GCUCCCaUUCCCugCCGCcUAG-UUCG- -5'
22307	5'	-55.1	NC_005045.1	+	74	0.75	0.217015
	Target:  5'- aCGGGGG-AAGGGugGGCGuGUCgGAGUc -3' miRNA:   3'- -GCUCCCaUUCCCugCCGCcUAG-UUCG- -5'
22307	5'	-55.1	NC_005045.1	+	8759	1.11	0.000555
	Target:  5'- aCGAGGGUAAGGGACGGCGGAUCAAGCc -3' miRNA:   3'- -GCUCCCAUUCCCUGCCGCCUAGUUCG- -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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