; matrix-scan -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/06/17/matrix-scan_2026-06-17.135617_55Tg2x.matrix -pseudo 1 -decimals 1 -2str -origin end -bgfile $RSAT/public_html/data/genomes/Escherichia_coli_str._K-12_substr._MG1655_GCF_000005845.2_ASM584v2/oligo-frequencies/2nt_upstream-noorf_Escherichia_coli_str._K-12_substr._MG1655_GCF_000005845.2_ASM584v2-ovlp-1str.freq -bg_pseudo 0.01 -return limits -return sites -return pval -return rank -lth score 1 -uth pval 1e-4 -i $RSAT/public_html/tmp/www-data/2026/06/17/tmp_sequence_2026-06-17.135617_LE6bZt.fasta -seq_format fasta -n score ; Slow counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/06/17/tmp_sequence_2026-06-17.135617_LE6bZt.fasta ; bg $RSAT/public_html/data/genomes/Escherichia_coli_str._K-12_substr._MG1655_GCF_000005845.2_ASM584v2/oligo-frequencies/2nt_upstream-noorf_Escherichia_coli_str._K-12_substr._MG1655_GCF_000005845.2_ASM584v2-ovlp-1str.freq ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/06/17/matrix-scan_2026-06-17.135617_55Tg2x.matrix ; Sequence format fasta ; Pseudo counts 1 ; Background model ; Method file ; Markov order 1 ; Strand sensitive ; Background pseudo-frequency 0.01 ; Residue probabilities ; a 0.29220 ; c 0.20695 ; g 0.20335 ; t 0.29751 ; Thresholds lower upper ; pval NA 0.0001 ; score 1 NA ; Output columns ; 1 seq_id ; 2 ft_type ; 3 ft_name ; 4 strand ; 5 start ; 6 end ; 7 sequence ; 8 weight #seq_id ft_type ft_name strand start end sequence weight Pval ln_Pval sig rank rank_pm ; ; Matrices ; matrix name ncol nrow pseudo Wmin Wmax Wrange ; 1 Ada 21 4 1 -32.400 15.700 48.100 a:0.292 c:0.207 g:0.203 t:0.298 ; 2 AgaR 22 4 1 -46.500 15.700 62.200 a:0.292 c:0.207 g:0.203 t:0.298 ; 3 ArgR 20 4 1 -41.900 14.400 56.300 a:0.292 c:0.207 g:0.203 t:0.298 ; 4 BaeR 18 4 1 -29.000 17.200 46.200 a:0.292 c:0.207 g:0.203 t:0.298 ; 5 BasR 20 4 1 -41.700 16.600 58.300 a:0.292 c:0.207 g:0.203 t:0.298 ; 6 BtsR 11 4 1 -19.100 8.000 27.100 a:0.292 c:0.207 g:0.203 t:0.298 ; 7 CaiF 16 4 1 -25.800 14.600 40.400 a:0.292 c:0.207 g:0.203 t:0.298 ; 8 CpxR 16 4 1 -19.800 9.300 29.100 a:0.292 c:0.207 g:0.203 t:0.298 ; 9 Cra 19 4 1 -45.600 17.000 62.600 a:0.292 c:0.207 g:0.203 t:0.298 ; 10 CRP 25 4 1 -25.100 16.400 41.500 a:0.292 c:0.207 g:0.203 t:0.298 ; 11 CsgD 17 4 1 -26.400 10.400 36.800 a:0.292 c:0.207 g:0.203 t:0.298 ; 12 CysB 39 4 1 -68.700 24.700 93.400 a:0.292 c:0.207 g:0.203 t:0.298 ; 13 CytR 15 4 1 -33.100 9.600 42.700 a:0.292 c:0.207 g:0.203 t:0.298 ; 14 Dan 7 4 1 -11.100 6.800 17.900 a:0.292 c:0.207 g:0.203 t:0.298 ; 15 DcuR 14 4 1 -28.600 9.700 38.300 a:0.292 c:0.207 g:0.203 t:0.298 ; 16 DeoR 19 4 1 -35.100 14.800 49.900 a:0.292 c:0.207 g:0.203 t:0.298 ; 17 DnaA 10 4 1 -22.600 8.700 31.300 a:0.292 c:0.207 g:0.203 t:0.298 ; 18 EvgA 20 4 1 -42.500 20.100 62.600 a:0.292 c:0.207 g:0.203 t:0.298 ; 19 ExuR 18 4 1 -39.800 16.200 56.000 a:0.292 c:0.207 g:0.203 t:0.298 ; 20 FadR 19 4 1 -40.200 17.000 57.200 a:0.292 c:0.207 g:0.203 t:0.298 ; 21 FeaR 20 4 1 -32.200 18.100 50.300 a:0.292 c:0.207 g:0.203 t:0.298 ; 22 FhlA 11 4 1 -21.200 10.300 31.500 a:0.292 c:0.207 g:0.203 t:0.298 ; 23 Fis 18 4 1 -16.300 9.600 25.900 a:0.292 c:0.207 g:0.203 t:0.298 ; 24 FlhDC 17 4 1 -30.000 12.900 42.900 a:0.292 c:0.207 g:0.203 t:0.298 ; 25 Fur 22 4 1 -36.000 17.800 53.800 a:0.292 c:0.207 g:0.203 t:0.298 ; Number of sequences scanned 0 ; Sum of sequence lengths 0 ; N residues 0 ; Matches per matrix ; matrix name matches scored ; 1 Ada 0 0 ; 2 AgaR 0 0 ; 3 ArgR 0 0 ; 4 BaeR 0 0 ; 5 BasR 0 0 ; 6 BtsR 0 0 ; 7 CaiF 0 0 ; 8 CpxR 0 0 ; 9 Cra 0 0 ; 10 CRP 0 0 ; 11 CsgD 0 0 ; 12 CysB 0 0 ; 13 CytR 0 0 ; 14 Dan 0 0 ; 15 DcuR 0 0 ; 16 DeoR 0 0 ; 17 DnaA 0 0 ; 18 EvgA 0 0 ; 19 ExuR 0 0 ; 20 FadR 0 0 ; 21 FeaR 0 0 ; 22 FhlA 0 0 ; 23 Fis 0 0 ; 24 FlhDC 0 0 ; 25 Fur 0 0 ; TOTAL 0 0 ; Host name rsat ; Job started 2026-06-17.135617 ; Job done 2026-06-17.135638 ; Seconds 20.53 ; user 20.53 ; system 0.04 ; cuser 0 ; csystem 0