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
3107	3'	-48.1	NC_001493.1	+	40304	0.66	0.999002
	Target:  5'- cUCCGC--CAGUaUGUUCguacACAUGUACUc -3' miRNA:   3'- -AGGCGaaGUCA-ACAAG----UGUACAUGGu -5'
3107	3'	-48.1	NC_001493.1	+	62166	0.66	0.999002
	Target:  5'- gUUCGCUUCAGUgucUUCACGg--GCUAu -3' miRNA:   3'- -AGGCGAAGUCAac-AAGUGUacaUGGU- -5'
3107	3'	-48.1	NC_001493.1	+	80956	0.68	0.994072
	Target:  5'- gUCCGCaacagcgCGGUUcUUCGCAcgGUACCGg -3' miRNA:   3'- -AGGCGaa-----GUCAAcAAGUGUa-CAUGGU- -5'
3107	3'	-48.1	NC_001493.1	+	114773	0.68	0.992024
	Target:  5'- aUCCGCUUCAcgcucGUcgaugauuuccUGgacgaaCACGUGUACCAu -3' miRNA:   3'- -AGGCGAAGU-----CA-----------ACaa----GUGUACAUGGU- -5'
3107	3'	-48.1	NC_001493.1	+	60195	0.69	0.988564
	Target:  5'- aUCCGCUggaucauccgaagggUCAGUg--UCGgGUGUGCCc -3' miRNA:   3'- -AGGCGA---------------AGUCAacaAGUgUACAUGGu -5'
3107	3'	-48.1	NC_001493.1	+	97357	0.7	0.972286
	Target:  5'- cCCGauucaCUUCAcc-GUUCACGUGUGCCAc -3' miRNA:   3'- aGGC-----GAAGUcaaCAAGUGUACAUGGU- -5'
3107	3'	-48.1	NC_001493.1	+	97156	1.1	0.011644
	Target:  5'- uUCCGCUUCAGUUGUUCACAUGUACCAu -3' miRNA:   3'- -AGGCGAAGUCAACAAGUGUACAUGGU- -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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