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
17964	5'	-54.9	NC_004665.1	+	16499	0.66	0.586802
	Target:  5'- -gUCCUUcUUGACCUUcagagaGUCGGUCCCa -3' miRNA:   3'- aaAGGGAuAGCUGGGG------UAGUCAGGGg -5'
17964	5'	-54.9	NC_004665.1	+	16666	0.67	0.530949
	Target:  5'- -cUCCCUca-GACgCUCAcgaaagaccgcUCGGUCCCCg -3' miRNA:   3'- aaAGGGAuagCUG-GGGU-----------AGUCAGGGG- -5'
17964	5'	-54.9	NC_004665.1	+	37294	0.68	0.487698
	Target:  5'- aUUCCCUcugaGUCcuGCCCCAUaauGaUCCCCa -3' miRNA:   3'- aAAGGGA----UAGc-UGGGGUAgu-C-AGGGG- -5'
17964	5'	-54.9	NC_004665.1	+	188	0.68	0.487698
	Target:  5'- aUUCCCUcugaGUCcuGCCCCAUaauGaUCCCCa -3' miRNA:   3'- aAAGGGA----UAGc-UGGGGUAgu-C-AGGGG- -5'
17964	5'	-54.9	NC_004665.1	+	205	0.68	0.4667
	Target:  5'- --cCCCUAUCuGuCCCUAUCuguaAGUCCUCc -3' miRNA:   3'- aaaGGGAUAG-CuGGGGUAG----UCAGGGG- -5'
17964	5'	-54.9	NC_004665.1	+	2515	0.74	0.202481
	Target:  5'- --aCCUUAUCGACCCCGgcaCAGUUCgCa -3' miRNA:   3'- aaaGGGAUAGCUGGGGUa--GUCAGGgG- -5'
17964	5'	-54.9	NC_004665.1	+	37339	1.1	0.000507
	Target:  5'- gUUUCCCUAUCGACCCCAUCAGUCCCCa -3' miRNA:   3'- -AAAGGGAUAGCUGGGGUAGUCAGGGG- -5'
17964	5'	-54.9	NC_004665.1	+	233	1.1	0.000507
	Target:  5'- gUUUCCCUAUCGACCCCAUCAGUCCCCa -3' miRNA:   3'- -AAAGGGAUAGCUGGGGUAGUCAGGGG- -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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