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
6153	3'	-57.4	NC_001829.1	+	1177	0.66	0.092889
	Target:  5'- -uGCCUCCAaaaucAUGaGCCugacaaagACGGCUccGGACUa -3' miRNA:   3'- ccUGGAGGU-----UAC-CGG--------UGCCGA--CCUGG- -5'
6153	3'	-57.4	NC_001829.1	+	1929	0.66	0.083925
	Target:  5'- cGGAagCUCCGGUGGacuaCGCGGaCaGGuACCa -3' miRNA:   3'- -CCUg-GAGGUUACCg---GUGCC-GaCC-UGG- -5'
6153	3'	-57.4	NC_001829.1	+	1135	0.66	0.080302
	Target:  5'- -cGCCUCCAacucgcggucacaaAUcaaGGCCGCG-CUGGACa -3' miRNA:   3'- ccUGGAGGU--------------UA---CCGGUGCcGACCUGg -5'
6153	3'	-57.4	NC_001829.1	+	860	0.7	0.036752
	Target:  5'- cGAgCUCCAGUGGgCGUGGacuaacaUGGACCa -3' miRNA:   3'- cCUgGAGGUUACCgGUGCCg------ACCUGG- -5'
6153	3'	-57.4	NC_001829.1	+	605	0.74	0.01959
	Target:  5'- aGGGCCUCCGG-GGCCuuacucacGCGGCgccacucGACCa -3' miRNA:   3'- -CCUGGAGGUUaCCGG--------UGCCGac-----CUGG- -5'
6153	3'	-57.4	NC_001829.1	+	1305	0.74	0.017023
	Target:  5'- cGGCCUCCGucuuCCugGGCUGGGCg -3' miRNA:   3'- cCUGGAGGUuaccGGugCCGACCUGg -5'
6153	3'	-57.4	NC_001829.1	+	3813	1.14	0.000006
	Target:  5'- cGGACCUCCAAUGGCCACGGCUGGACCu -3' miRNA:   3'- -CCUGGAGGUUACCGGUGCCGACCUGG- -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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