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
22861	5'	-47.3	NC_005137.2	+	11377	0.66	0.999343
	Target:  5'- --cACgGCGCCaUUGGgGUUuGUGGUGg -3' miRNA:   3'- guuUGgCGUGGaAACUgCAA-CAUCAC- -5'
22861	5'	-47.3	NC_005137.2	+	130051	0.67	0.999184
	Target:  5'- aAAGCCGCGCCUUauugcgccgaUGACGggcgcUGGUc -3' miRNA:   3'- gUUUGGCGUGGAA----------ACUGCaac--AUCAc -5'
22861	5'	-47.3	NC_005137.2	+	100558	0.67	0.998664
	Target:  5'- aCGAGCCGCGCagcagaaccGCGUUGUcgAGUGc -3' miRNA:   3'- -GUUUGGCGUGgaaac----UGCAACA--UCAC- -5'
22861	5'	-47.3	NC_005137.2	+	83690	0.7	0.984201
	Target:  5'- aCAAACCGUacaGCCUUUGAUaaucuUUGUGGUu -3' miRNA:   3'- -GUUUGGCG---UGGAAACUGc----AACAUCAc -5'
22861	5'	-47.3	NC_005137.2	+	20984	0.74	0.921584
	Target:  5'- --uGCCGCGCUugcacgcaaacgggUUUGACGUaGUAGUGu -3' miRNA:   3'- guuUGGCGUGG--------------AAACUGCAaCAUCAC- -5'
22861	5'	-47.3	NC_005137.2	+	95571	0.76	0.824533
	Target:  5'- uCAAACgGCAgCgugUUGGCGUUGUAGUu -3' miRNA:   3'- -GUUUGgCGUgGa--AACUGCAACAUCAc -5'
22861	5'	-47.3	NC_005137.2	+	118067	1.11	0.013112
	Target:  5'- aCAAACCGCACCUUUGACGUUGUAGUGg -3' miRNA:   3'- -GUUUGGCGUGGAAACUGCAACAUCAC- -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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