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
4360	3'	-54	NC_001720.1	+	36411	0.66	0.72605
	Target:  5'- gGAGCUcucuggaaaaaucGCGGGCUCUUAUacacuuacUCuccGCCCa -3' miRNA:   3'- gCUUGA-------------CGUCCGAGAGUA--------AGuc-CGGG- -5'
4360	3'	-54	NC_001720.1	+	21750	0.67	0.659079
	Target:  5'- gGAGCUGUuuacugccgugauGGGUUCU---UCAGaGCCCa -3' miRNA:   3'- gCUUGACG-------------UCCGAGAguaAGUC-CGGG- -5'
4360	3'	-54	NC_001720.1	+	7030	0.69	0.519008
	Target:  5'- cCGAGCUguacgugucacuuccGCAGGCUUugcacuugaugUCGcaaucgCAGGCCCa -3' miRNA:   3'- -GCUUGA---------------CGUCCGAG-----------AGUaa----GUCCGGG- -5'
4360	3'	-54	NC_001720.1	+	18307	0.7	0.441543
	Target:  5'- cCGcGGCUGCAGuaCUUUCAUaucgCGGGCCCu -3' miRNA:   3'- -GC-UUGACGUCc-GAGAGUAa---GUCCGGG- -5'
4360	3'	-54	NC_001720.1	+	37517	0.72	0.36569
	Target:  5'- gCGAgcaACUGCGGGaauaCUCAUUCAG-CCCc -3' miRNA:   3'- -GCU---UGACGUCCga--GAGUAAGUCcGGG- -5'
4360	3'	-54	NC_001720.1	+	26159	0.77	0.18469
	Target:  5'- cCGAugUGguGGuCUCUCA---GGGCCCa -3' miRNA:   3'- -GCUugACguCC-GAGAGUaagUCCGGG- -5'
4360	3'	-54	NC_001720.1	+	17897	1.12	0.000548
	Target:  5'- cCGAACUGCAGGCUCUCAUUCAGGCCCu -3' miRNA:   3'- -GCUUGACGUCCGAGAGUAAGUCCGGG- -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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