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
12751	5'	-52.2	NC_003356.1	+	36666	0.66	0.848071
	Target:  5'- -gCCAgguAAAAAGCGAaauaaucacagcaCGCGUCagaaggucgagcgaaGCCCCGg -3' miRNA:   3'- agGGU---UUUUUUGCU-------------GCGCAG---------------CGGGGC- -5'
12751	5'	-52.2	NC_003356.1	+	25586	0.67	0.781994
	Target:  5'- cUCCAGAAaugGAGCGAaaaaaaggcgcugccUGCGUUGCUCUGg -3' miRNA:   3'- aGGGUUUU---UUUGCU---------------GCGCAGCGGGGC- -5'
12751	5'	-52.2	NC_003356.1	+	19267	0.67	0.777885
	Target:  5'- aUCCCGAAAuccguuccgguAAACaGCccgaauacCGUCGCCCCGc -3' miRNA:   3'- -AGGGUUUU-----------UUUGcUGc-------GCAGCGGGGC- -5'
12751	5'	-52.2	NC_003356.1	+	33499	0.68	0.746308
	Target:  5'- uUCCCG-----GCGGCGCGUUGUCaaaCGu -3' miRNA:   3'- -AGGGUuuuuuUGCUGCGCAGCGGg--GC- -5'
12751	5'	-52.2	NC_003356.1	+	18906	0.68	0.73552
	Target:  5'- aCCCAacuacagaccAAAAAGgGGCGUGaaCGCCCCu -3' miRNA:   3'- aGGGU----------UUUUUUgCUGCGCa-GCGGGGc -5'
12751	5'	-52.2	NC_003356.1	+	22897	0.82	0.116461
	Target:  5'- aUCCCG--GAGACGGCGCGUCGCCg-- -3' miRNA:   3'- -AGGGUuuUUUUGCUGCGCAGCGGggc -5'
12751	5'	-52.2	NC_003356.1	+	28286	1.11	0.00129
	Target:  5'- uUCCCAAAAAAACGACGCGUCGCCCCGg -3' miRNA:   3'- -AGGGUUUUUUUGCUGCGCAGCGGGGC- -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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