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
18024	3'	-59	NC_004665.1	+	36866	0.66	0.443089
	Target:  5'- aGCUggGUCuCCAcCCucguguguGuGGCCUCUGGc -3' miRNA:   3'- gCGGuuCAGcGGUuGG--------C-CCGGAGACC- -5'
18024	3'	-59	NC_004665.1	+	19906	0.66	0.443089
	Target:  5'- aGCUcgAAG-CGCCcACuCGGGCCUCg-- -3' miRNA:   3'- gCGG--UUCaGCGGuUG-GCCCGGAGacc -5'
18024	3'	-59	NC_004665.1	+	16897	0.66	0.433423
	Target:  5'- --gCAGGUUcCCGcUgGGGCCUCUGGa -3' miRNA:   3'- gcgGUUCAGcGGUuGgCCCGGAGACC- -5'
18024	3'	-59	NC_004665.1	+	31411	0.66	0.405182
	Target:  5'- -aCCAAGUaggUGCgAACUcugaGGGUCUCUGGa -3' miRNA:   3'- gcGGUUCA---GCGgUUGG----CCCGGAGACC- -5'
18024	3'	-59	NC_004665.1	+	31033	0.67	0.359926
	Target:  5'- uCGCUAuucaaggGGUCGUCGcaaCGGGCCUCgcaacGGg -3' miRNA:   3'- -GCGGU-------UCAGCGGUug-GCCCGGAGa----CC- -5'
18024	3'	-59	NC_004665.1	+	3358	0.68	0.31213
	Target:  5'- uCGCCGaggaacaucaGGUCGauucGCCGGGUCUCgGGa -3' miRNA:   3'- -GCGGU----------UCAGCggu-UGGCCCGGAGaCC- -5'
18024	3'	-59	NC_004665.1	+	7407	0.68	0.311362
	Target:  5'- uGCCGaagcccuucucagGGUUGCCGAagUCaGGCUUCUGGa -3' miRNA:   3'- gCGGU-------------UCAGCGGUU--GGcCCGGAGACC- -5'
18024	3'	-59	NC_004665.1	+	4360	0.68	0.297059
	Target:  5'- uCGCCAAGaucgccUCGCCAgaagcucuggugACCGacguGGCCuucUCUGGg -3' miRNA:   3'- -GCGGUUC------AGCGGU------------UGGC----CCGG---AGACC- -5'
18024	3'	-59	NC_004665.1	+	27139	0.7	0.255251
	Target:  5'- uGCUggGUCaGCCAugaGGGCCUUcuUGGa -3' miRNA:   3'- gCGGuuCAG-CGGUuggCCCGGAG--ACC- -5'
18024	3'	-59	NC_004665.1	+	20327	0.74	0.134126
	Target:  5'- uGCCGAGUacagCGcCCAACUGGGUgaagCUCUGGc -3' miRNA:   3'- gCGGUUCA----GC-GGUUGGCCCG----GAGACC- -5'
18024	3'	-59	NC_004665.1	+	27554	1.11	0.000191
	Target:  5'- aCGCCAAGUCGCCAACCGGGCCUCUGGg -3' miRNA:   3'- -GCGGUUCAGCGGUUGGCCCGGAGACC- -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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