; matrix-scan -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/04/21/matrix-scan_2026-04-21.105757_bnR4Dx.matrix -pseudo 1 -decimals 1 -2str -origin end -bginput -markov 1 -bg_pseudo 0.01 -n skip -return crer -return limits -return sites -lth crer_size 30 -uth crer_size 500 -lth crer_sig 2 -uth pval 1e-3 -i $RSAT/public_html/tmp/www-data/2026/04/21/tmp_sequence_2026-04-21.105757_am6Usz.fasta -seq_format fasta -n score ; Slow counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/04/21/tmp_sequence_2026-04-21.105757_am6Usz.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/04/21/matrix-scan_2026-04-21.105757_bnR4Dx.matrix ; Sequence format fasta ; Pseudo counts 1 ; Background model ; Method input ; Markov order 1 ; Strand undef ; Background pseudo-frequency 0.01 ; Residue probabilities ; a 0.32898 ; c 0.16801 ; g 0.21121 ; t 0.29180 ; Thresholds lower upper ; crer_sig 2 NA ; crer_size 30 500 ; pval NA 0.001 ; 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 #seq_id ft_type ft_name strand start end hit_sum crer_sig crer_pval hit_pval_product weight_sum crer_size PqseB_upstream_500bp limit START_END D -500 -1 . 0 0 0 0 PqseB_upstream_500bp CRER crer DR -294 -24 1 2.027 9.4e-03 3.1e-44 69.5 271 PqseB_upstream_500bp CRER crer DR -294 -19 1 2.358 4.4e-03 1.7e-47 74.7 276 PqseB_upstream_500bp CRER crer DR -211 -130 1 2.318 4.8e-03 1.4e-21 32.8 82 PqseB_upstream_500bp CRER crer DR -211 -80 1 2.135 7.3e-03 8.2e-28 42.5 132 PqseB_upstream_500bp CRER crer DR -211 -75 1 2.605 2.5e-03 2.5e-31 48.4 137 PqseB_upstream_500bp CRER crer DR -211 -45 1 2.592 2.6e-03 8.6e-35 54.3 167 PqseB_upstream_500bp CRER crer DR -211 -22 1 2.659 2.2e-03 6.0e-38 59.3 190 PqseB_upstream_500bp CRER crer DR -211 -24 1 2.976 1.1e-03 5.8e-41 64.1 188 PqseB_upstream_500bp CRER crer DR -211 -19 1 3.411 3.9e-04 3.2e-44 69.3 193 PqseB_upstream_500bp CRER crer DR -200 -130 1 2.009 9.8e-03 9.2e-18 26.5 71 PqseB_upstream_500bp CRER crer DR -200 -75 1 2.315 4.8e-03 1.6e-27 42.1 126 PqseB_upstream_500bp CRER crer DR -200 -45 1 2.311 4.9e-03 5.7e-31 48 156 PqseB_upstream_500bp CRER crer DR -200 -22 1 2.385 4.1e-03 4.0e-34 53 179 PqseB_upstream_500bp CRER crer DR -200 -24 1 2.700 2.0e-03 3.9e-37 57.8 177 PqseB_upstream_500bp CRER crer DR -200 -19 1 3.131 7.4e-04 2.1e-40 63 182 PqseB_upstream_500bp CRER crer DR -172 -130 1 2.444 3.6e-03 1.5e-10 15.3 43 PqseB_upstream_500bp CRER crer DR -172 -75 1 2.467 3.4e-03 2.6e-20 30.9 98 PqseB_upstream_500bp CRER crer DR -172 -45 1 2.413 3.9e-03 9.2e-24 36.8 128 PqseB_upstream_500bp CRER crer DR -172 -22 1 2.464 3.4e-03 6.4e-27 41.8 151 PqseB_upstream_500bp CRER crer DR -172 -24 1 2.797 1.6e-03 6.3e-30 46.6 149 PqseB_upstream_500bp CRER crer DR -172 -19 1 3.259 5.5e-04 3.4e-33 51.8 154 PqseB_upstream_500bp CRER crer DR -171 -24 1 2.290 5.1e-03 3.1e-30 46.9 148 PqseB_upstream_500bp CRER crer DR -171 -19 1 2.726 1.9e-03 1.7e-33 52.1 153 PqseB_upstream_500bp CRER crer DR -150 -24 1 2.223 6.0e-03 3.8e-23 36 127 PqseB_upstream_500bp CRER crer DR -150 -19 1 2.680 2.1e-03 2.1e-26 41.2 132 PqseB_upstream_500bp CRER crer DR -146 -19 1 2.223 6.0e-03 8.1e-27 42.3 128 PqseB_upstream_500bp CRER crer DR -105 -75 1 2.309 4.9e-03 2.8e-07 10.5 31 PqseB_upstream_500bp CRER crer DR -105 -24 1 2.224 6.0e-03 6.7e-17 26.2 82 PqseB_upstream_500bp CRER crer DR -105 -19 1 2.756 1.8e-03 3.7e-20 31.4 87 PqseB_upstream_500bp CRER crer DR -94 -19 1 2.453 3.5e-03 8.2e-17 26 76 PqseB_upstream_500bp CRER crer DR -67 -19 1 2.035 9.2e-03 1.3e-13 20.9 49 PqseB_upstream_500bp site Lrp R -494 -480 CGGAGTAATAATTCG 5.6 3.0e-04 -8.103 3.519 PqseB_upstream_500bp site OxyR D -459 -441 ACAAATCTTGGCAATCTTA 5.3 6.2e-04 -7.389 3.209 PqseB_upstream_500bp site IHF R -440 -427 ATATCCTTTAGTTC 4.8 9.7e-04 -6.936 3.012 PqseB_upstream_500bp site Lrp R -434 -420 CAGCATCATATCCTT 4.8 9.6e-04 -6.946 3.016 PqseB_upstream_500bp site H-NS R -415 -404 ATTTCATAAGAT 5.3 1.8e-04 -8.628 3.747 PqseB_upstream_500bp site OxyR D -294 -276 ACAACTCTTTCCTATACAT 5.4 5.4e-04 -7.521 3.266 PqseB_upstream_500bp site OxyR R -211 -193 ATCGCCACTTCTAGTCGTA 6.3 1.5e-04 -8.796 3.820 PqseB_upstream_500bp site OmpR R -200 -178 TTTACGAATTCTTCCATCGCCAC 6.1 2.7e-04 -8.218 3.569 PqseB_upstream_500bp site NarL D -172 -163 CTACGGAGTA 4.8 4.7e-04 -7.671 3.332 PqseB_upstream_500bp site NarL R -171 -162 GTACTCCGTA 5.1 2.3e-04 -8.385 3.641 PqseB_upstream_500bp site CRP R -150 -126 CATCTTTGAGTAATCTCAGATTAGC 4.7 9.0e-04 -7.008 3.044 PqseB_upstream_500bp site FNR R -146 -130 TTTGAGTAATCTCAGAT 5.8 3.5e-04 -7.966 3.459 PqseB_upstream_500bp site Fur R -105 -84 GTTTATTTCCAATATTATTAAT 4.6 9.4e-04 -6.974 3.029 PqseB_upstream_500bp site Lrp R -94 -80 TATCGTTTATTTCCA 5.1 6.3e-04 -7.373 3.202 PqseB_upstream_500bp site FNR R -91 -75 TTTGATATCGTTTATTT 5.9 3.0e-04 -8.107 3.521 PqseB_upstream_500bp site OmpR D -67 -45 CCAACGTTTGCATTCACATATAA 5.9 3.5e-04 -7.971 3.462 PqseB_upstream_500bp site CRP D -46 -22 AAACCCTGGTCGTCAGTACATTATT 5.0 7.0e-04 -7.269 3.157 PqseB_upstream_500bp site IHF D -37 -24 TCGTCAGTACATTA 4.8 9.7e-04 -6.936 3.012 PqseB_upstream_500bp site Lrp R -33 -19 CCCAATAATGTACTG 5.2 5.5e-04 -7.500 3.257 ; ; Matrices ; matrix name ncol nrow pseudo Wmin Wmax Wrange ; 1 ArcA 16 4 1 -28.600 10.200 38.800 a:0.329 c:0.168 g:0.211 t:0.292 ; 2 CRP 25 4 1 -24.700 16.300 41.000 a:0.329 c:0.168 g:0.211 t:0.292 ; 3 Fis 18 4 1 -15.600 9.400 25.000 a:0.329 c:0.168 g:0.211 t:0.292 ; 4 FNR 17 4 1 -17.000 11.000 28.000 a:0.329 c:0.168 g:0.211 t:0.292 ; 5 Fur 22 4 1 -35.600 17.500 53.100 a:0.329 c:0.168 g:0.211 t:0.292 ; 6 H-NS 12 4 1 -27.000 6.300 33.300 a:0.329 c:0.168 g:0.211 t:0.292 ; 7 IHF 14 4 1 -19.000 7.800 26.800 a:0.329 c:0.168 g:0.211 t:0.292 ; 8 Lrp 15 4 1 -16.400 10.100 26.500 a:0.329 c:0.168 g:0.211 t:0.292 ; 9 NarL 10 4 1 -11.900 6.400 18.300 a:0.329 c:0.168 g:0.211 t:0.292 ; 10 NarP 13 4 1 -27.500 10.800 38.300 a:0.329 c:0.168 g:0.211 t:0.292 ; 11 OmpR 23 4 1 -35.300 13.600 48.900 a:0.329 c:0.168 g:0.211 t:0.292 ; 12 OxyR 19 4 1 -26.000 12.000 38.000 a:0.329 c:0.168 g:0.211 t:0.292 ; Number of sequences scanned 1 ; Sum of sequence lengths 500 ; N residues 0 ; Matches per matrix ; matrix name matches scored ; 1 ArcA 0 970 ; 2 CRP 2 952 ; 3 Fis 0 966 ; 4 FNR 2 968 ; 5 Fur 1 958 ; 6 H-NS 1 978 ; 7 IHF 2 974 ; 8 Lrp 4 972 ; 9 NarL 2 982 ; 10 NarP 0 976 ; 11 OmpR 2 956 ; 12 OxyR 3 964 ; TOTAL 19 11616 ; Number of Binomial tests per sequence (can be used for multi-testing correction) ; sequence number of tests ; PqseB_upstream_500bp 163 ; TOTAL 163 ; Host name rsat ; Job started 2026-04-21.105757 ; Job done 2026-04-21.105805 ; Seconds 7.42 ; user 7.42 ; system 0.02 ; cuser 0.11 ; csystem 0.02