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
22154	3'	-61.1	NC_004927.1	+	6403	0.66	0.535459
	Target:  5'- --uUCCUcaCACCGGAGCuuugaGCCGCCa-- -3' miRNA:   3'- cgcAGGAa-GUGGCCUCG-----CGGCGGccu -5'
22154	3'	-61.1	NC_004927.1	+	21111	0.66	0.52555
	Target:  5'- uGCGcUCCUcgaagUCGCCGcucGCGCCGCUGu- -3' miRNA:   3'- -CGC-AGGA-----AGUGGCcu-CGCGGCGGCcu -5'
22154	3'	-61.1	NC_004927.1	+	3373	0.66	0.52555
	Target:  5'- uCGUUaugguaGCUGGAguaGCGCCGCCGGu -3' miRNA:   3'- cGCAGgaag--UGGCCU---CGCGGCGGCCu -5'
22154	3'	-61.1	NC_004927.1	+	34843	0.68	0.431068
	Target:  5'- aGCGgCCaUCACgGGAaCGUCGUCGGGg -3' miRNA:   3'- -CGCaGGaAGUGgCCUcGCGGCGGCCU- -5'
22154	3'	-61.1	NC_004927.1	+	36432	0.7	0.315022
	Target:  5'- aGCGagccauUCCUUCGCCGucucuaucgggucaGAGUGuuGCCGGu -3' miRNA:   3'- -CGC------AGGAAGUGGC--------------CUCGCggCGGCCu -5'
22154	3'	-61.1	NC_004927.1	+	36119	0.7	0.302904
	Target:  5'- aGCGUCCccacUUCACCGGAaaCGCCGUCu-- -3' miRNA:   3'- -CGCAGG----AAGUGGCCUc-GCGGCGGccu -5'
22154	3'	-61.1	NC_004927.1	+	21826	0.71	0.268715
	Target:  5'- uCGUCac-CGCCGGAGUcgccaccgagcgaGCCGCUGGAg -3' miRNA:   3'- cGCAGgaaGUGGCCUCG-------------CGGCGGCCU- -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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