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
18448	5'	-53.8	NC_004681.1	+	49719	0.66	0.890052
	Target:  5'- uUCUCGUUCACcGGACgacgacgggaaucugCGCCuuCUUGg -3' miRNA:   3'- cAGAGCAAGUGcCCUG---------------GUGGuuGAGC- -5'
18448	5'	-53.8	NC_004681.1	+	56317	0.66	0.887182
	Target:  5'- -gCUCGggUCGacgcCGGuccaGGCCACCGACUCa -3' miRNA:   3'- caGAGCa-AGU----GCC----CUGGUGGUUGAGc -5'
18448	5'	-53.8	NC_004681.1	+	8444	0.68	0.803486
	Target:  5'- cGUCUCGUUCaACGuGAgCGCCAAggCGg -3' miRNA:   3'- -CAGAGCAAG-UGCcCUgGUGGUUgaGC- -5'
18448	5'	-53.8	NC_004681.1	+	61067	0.68	0.764679
	Target:  5'- aUCUCGUcggCACGcuGACCGCCGACccCGa -3' miRNA:   3'- cAGAGCAa--GUGCc-CUGGUGGUUGa-GC- -5'
18448	5'	-53.8	NC_004681.1	+	46916	0.71	0.631962
	Target:  5'- -aCUgGUUCGCuGGcacuaccuacggugaGGCCGCCGACUCGg -3' miRNA:   3'- caGAgCAAGUG-CC---------------CUGGUGGUUGAGC- -5'
18448	5'	-53.8	NC_004681.1	+	42348	0.72	0.563253
	Target:  5'- uUCcgCGg--GCGGGACCAgCAGCUCGg -3' miRNA:   3'- cAGa-GCaagUGCCCUGGUgGUUGAGC- -5'
18448	5'	-53.8	NC_004681.1	+	36605	1.1	0.00214
	Target:  5'- uGUCUCGUUCACGGGACCACCAACUCGg -3' miRNA:   3'- -CAGAGCAAGUGCCCUGGUGGUUGAGC- -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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