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
20691	3'	-56.1	NC_004688.1	+	80359	0.66	0.816003
	Target:  5'- -gGgGCCUCuUCGG-CCUUGCCGUCg -3' miRNA:   3'- uaUgUGGAGcAGUUgGGGACGGCAGa -5'
20691	3'	-56.1	NC_004688.1	+	25179	0.67	0.792253
	Target:  5'- -aGCAUCUCaaugcgacccauguaGUCAuggaguucGCCCCUGCCGcCg -3' miRNA:   3'- uaUGUGGAG---------------CAGU--------UGGGGACGGCaGa -5'
20691	3'	-56.1	NC_004688.1	+	40498	0.67	0.759664
	Target:  5'- -gACGCCUCGaCGACCUCggugagGCCGa-- -3' miRNA:   3'- uaUGUGGAGCaGUUGGGGa-----CGGCaga -5'
20691	3'	-56.1	NC_004688.1	+	67985	0.68	0.739823
	Target:  5'- -gACACCUCGUagaGGCCCUcguaGCCGggggCUg -3' miRNA:   3'- uaUGUGGAGCAg--UUGGGGa---CGGCa---GA- -5'
20691	3'	-56.1	NC_004688.1	+	85110	0.68	0.719586
	Target:  5'- -gACgACCUCGUUcGCCCCgccgggGCCGcCUu -3' miRNA:   3'- uaUG-UGGAGCAGuUGGGGa-----CGGCaGA- -5'
20691	3'	-56.1	NC_004688.1	+	79415	0.69	0.636245
	Target:  5'- -aGCugCUCGUgGAUgCCUGCUGUUc -3' miRNA:   3'- uaUGugGAGCAgUUGgGGACGGCAGa -5'
20691	3'	-56.1	NC_004688.1	+	109639	0.7	0.625716
	Target:  5'- -cGCGCCUCGUCGACCCauaagaGCUccggaGUCg -3' miRNA:   3'- uaUGUGGAGCAGUUGGGga----CGG-----CAGa -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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