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
22131	3'	-56.1	NC_004927.1	+	30653	0.66	0.765006
	Target:  5'- gGCuUGACGCCCUUCggaacCACGauaacaaCGuCAGCg -3' miRNA:   3'- -CG-GCUGCGGGAAGaa---GUGCg------GC-GUUG- -5'
22131	3'	-56.1	NC_004927.1	+	15079	0.66	0.75504
	Target:  5'- cUCGuCGCCCgUgUUCGgagcgaagccCGCCGCGACu -3' miRNA:   3'- cGGCuGCGGGaAgAAGU----------GCGGCGUUG- -5'
22131	3'	-56.1	NC_004927.1	+	75082	0.67	0.724472
	Target:  5'- aGUC-AUGUCCUUCUUCAa-UCGCAACa -3' miRNA:   3'- -CGGcUGCGGGAAGAAGUgcGGCGUUG- -5'
22131	3'	-56.1	NC_004927.1	+	70840	0.67	0.703641
	Target:  5'- cGCCGGuCGCCCUUCU--ACuCCaCAACu -3' miRNA:   3'- -CGGCU-GCGGGAAGAagUGcGGcGUUG- -5'
22131	3'	-56.1	NC_004927.1	+	61396	0.68	0.607792
	Target:  5'- gGCUGGCGCgauugaCUUCUUCGCuCCGCu-- -3' miRNA:   3'- -CGGCUGCGg-----GAAGAAGUGcGGCGuug -5'
22131	3'	-56.1	NC_004927.1	+	34238	0.69	0.597121
	Target:  5'- gGCCGcucggggcgaaGCGCCCUUCggCGUGCCGuCAGu -3' miRNA:   3'- -CGGC-----------UGCGGGAAGaaGUGCGGC-GUUg -5'
22131	3'	-56.1	NC_004927.1	+	47429	0.71	0.473318
	Target:  5'- uGCCGAacaGCCCgacgCUgaugaACGCCGgGACg -3' miRNA:   3'- -CGGCUg--CGGGaa--GAag---UGCGGCgUUG- -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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