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
19363	3'	-51.6	NC_004685.1	+	12482	0.66	0.933239
	Target:  5'- uGGCGCGCGcugaaggaUCGGGUGgUGCgcgaGGa -3' miRNA:   3'- uUCGCGCGCa-------AGCUCAUgAUGaag-CC- -5'
19363	3'	-51.6	NC_004685.1	+	45759	0.66	0.933239
	Target:  5'- cGGCGCGUGUUCGcugcgcGGUAC-ACcUCGc -3' miRNA:   3'- uUCGCGCGCAAGC------UCAUGaUGaAGCc -5'
19363	3'	-51.6	NC_004685.1	+	21614	0.66	0.932692
	Target:  5'- -cGC-CGCGaUCGAGUGCUucgagcaGCgggUCGGc -3' miRNA:   3'- uuCGcGCGCaAGCUCAUGA-------UGa--AGCC- -5'
19363	3'	-51.6	NC_004685.1	+	41248	0.66	0.927647
	Target:  5'- -cGCGCGCGUUCggcuuggucgcgGAGuUGCUugUgggUGGc -3' miRNA:   3'- uuCGCGCGCAAG------------CUC-AUGAugAa--GCC- -5'
19363	3'	-51.6	NC_004685.1	+	16038	0.67	0.902479
	Target:  5'- aGGGCGCGCGccgCGAaUACcGCaUCGGc -3' miRNA:   3'- -UUCGCGCGCaa-GCUcAUGaUGaAGCC- -5'
19363	3'	-51.6	NC_004685.1	+	25236	0.68	0.864907
	Target:  5'- cAGCGCGCaGgugaCGAGgACUGCggCGGu -3' miRNA:   3'- uUCGCGCG-Caa--GCUCaUGAUGaaGCC- -5'
19363	3'	-51.6	NC_004685.1	+	12915	1.08	0.003763
	Target:  5'- gAAGCGCGCGUUCGAGUACUACUUCGGc -3' miRNA:   3'- -UUCGCGCGCAAGCUCAUGAUGAAGCC- -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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