; matrix-scan -v 1 -matrix_format tab -m $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.193925_JtZruc.matrix -pseudo 1 -decimals 1 -2str -origin end -bginput -markov 1 -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/2026/04/30/retrieve-seq_2026-04-30.193419_fEUhtg.fasta.fasta.fasta -seq_format fasta -n score ; Slow counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/04/30/retrieve-seq_2026-04-30.193419_fEUhtg.fasta.fasta.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.193925_JtZruc.matrix ; Sequence format fasta ; Pseudo counts 1 ; Background model ; Method input ; Markov order 1 ; Strand undef ; Background pseudo-frequency 0.01 ; Residue probabilities ; a 0.30335 ; c 0.19690 ; g 0.19856 ; t 0.30118 ; 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 insA limit START_END D -106 -1 . 0 0 0 0 insA site matrix-scan_2026-04-30.3 D -34 -18 CAGCTGTCCCTCCTGTT 10.4 1.4e-06 -13.461 5.846 1 1 borD limit START_END D -341 -1 . 0 0 0 0 borD site matrix-scan_2026-04-30.5 R -120 -104 TAAACAAACCCTAAACA 10.9 7.7e-07 -14.083 6.116 1 1 borD site matrix-scan_2026-04-30.6 D -117 -101 TTAGGGTTTGTTTAATT 10.6 9.3e-07 -13.886 6.031 2 1 borD site matrix-scan_2026-04-30.4 D -162 -146 GCATACATTAATAAATA 10.5 1.0e-06 -13.772 5.981 3 1 borD site matrix-scan_2026-04-30.6 D -116 -100 TAGGGTTTGTTTAATTT 10.5 1.1e-06 -13.681 5.942 4 2 borD site matrix-scan_2026-04-30.3 D -27 -11 GCGCTGGCCCTGCTTAT 10.2 2.1e-06 -13.082 5.681 5 1 borD site matrix-scan_2026-04-30.5 R -119 -103 TTAAACAAACCCTAAAC 9.9 4.6e-06 -12.284 5.335 6 2 borD site matrix-scan_2026-04-30.3 D -270 -254 CCTGTGTGCATCGTTTT 9.2 1.0e-05 -11.488 4.989 7 2 ompT limit START_END D -474 -1 . 0 0 0 0 ompT site matrix-scan_2026-04-30.2 D -348 -332 CTTTTTTGTACTAAAAA 9.6 3.9e-06 -12.449 5.406 1 1 ompT site matrix-scan_2026-04-30.5 D -151 -135 TAAACAAAATATAAACA 9.9 4.6e-06 -12.284 5.335 2 1 ompT site matrix-scan_2026-04-30.2 R -346 -330 GTTTTTTAGTACAAAAA 9.5 4.8e-06 -12.257 5.323 3 2 ompT site matrix-scan_2026-04-30.3 R -259 -243 GCTTTTGTGGTGCTTTT 9.7 4.8e-06 -12.242 5.317 4 1 ompT site matrix-scan_2026-04-30.4 D -162 -146 TCATTCAATACTAAACA 9.1 1.1e-05 -11.438 4.968 5 1 ompT site matrix-scan_2026-04-30.4 R -168 -152 GTATTGAATGATTATCA 8.4 2.7e-05 -10.504 4.562 6 2 ompT site matrix-scan_2026-04-30.2 R -347 -331 TTTTTTAGTACAAAAAA 8.3 3.5e-05 -10.265 4.458 7 3 ompT site matrix-scan_2026-04-30.4 D -106 -90 GTTAGATATAAAAAATA 7.6 7.2e-05 -9.539 4.143 8 3 ompT site matrix-scan_2026-04-30.3 D -359 -343 GTTTTGTCCCTCTTTTT 7.4 9.4e-05 -9.269 4.026 9 2 ybeF limit START_END D -309 -1 . 0 0 0 0 ybeF site matrix-scan_2026-04-30.4 R -83 -67 TTATTCATGGAAAAATA 10.3 1.5e-06 -13.394 5.817 1 1 ybeF site matrix-scan_2026-04-30.2 D -83 -67 TATTTTTCCATGAATAA 9.2 8.5e-06 -11.679 5.072 2 1 ybeF site matrix-scan_2026-04-30.6 D -239 -223 TCGCGTTTGTATATTTT 8.7 2.1e-05 -10.765 4.675 3 1 ybeF site matrix-scan_2026-04-30.2 R -80 -64 ATTTTATTCATGGAAAA 7.9 5.9e-05 -9.730 4.226 4 2 ybeF site matrix-scan_2026-04-30.2 R -81 -65 TTTTATTCATGGAAAAA 7.8 6.8e-05 -9.598 4.168 5 3 ybeF site matrix-scan_2026-04-30.6 D -233 -217 TTGTATATTTTCTTTAT 7.4 9.7e-05 -9.237 4.011 6 2 ybjX limit START_END D -165 -1 . 0 0 0 0 ybjX site matrix-scan_2026-04-30.5 D -112 -96 TCAACAAAACCCTAAAA 10.0 3.9e-06 -12.444 5.405 1 1 ybjX site matrix-scan_2026-04-30.6 R -115 -99 TAGGGTTTTGTTGATAT 9.3 8.9e-06 -11.628 5.050 2 1 ybjX site matrix-scan_2026-04-30.6 R -114 -98 TTAGGGTTTTGTTGATA 8.2 4.0e-05 -10.133 4.401 3 2 ybjX site matrix-scan_2026-04-30.5 R -76 -60 TTAACCAAACATCAATA 7.6 8.3e-05 -9.401 4.083 4 2 nudJ limit START_END D -60 -1 . 0 0 0 0 yncH limit START_END D -126 -1 . 0 0 0 0 yncH site matrix-scan_2026-04-30.4 R -104 -88 TTACTGAATAATAAATA 9.5 5.8e-06 -12.050 5.233 1 1 yncH site matrix-scan_2026-04-30.5 R -53 -37 TAAAAAACATACCATGA 9.2 1.3e-05 -11.243 4.883 2 1 yncH site matrix-scan_2026-04-30.4 R -45 -29 ATATAAATTAAAAAACA 7.3 1.0e-04 -9.205 3.998 3 2 gadC limit START_END D -206 -1 . 0 0 0 0 gadB limit START_END D -412 -1 . 0 0 0 0 gadB site matrix-scan_2026-04-30.2 D -201 -185 TGTTTTTCAATGAAAAA 9.7 3.1e-06 -12.696 5.514 1 1 gadB site matrix-scan_2026-04-30.6 D -150 -134 TTAGGATTTTGTTATTT 9.8 4.1e-06 -12.409 5.389 2 1 gadB site matrix-scan_2026-04-30.5 R -212 -196 AAAACAATACAATATGA 9.9 4.6e-06 -12.284 5.335 3 1 gadB site matrix-scan_2026-04-30.6 D -149 -133 TAGGATTTTGTTATTTA 9.5 6.6e-06 -11.934 5.183 4 2 gadB site matrix-scan_2026-04-30.2 R -198 -182 TATTTTTTCATTGAAAA 8.9 1.4e-05 -11.168 4.850 5 2 gadB site matrix-scan_2026-04-30.5 R -152 -136 ATAACAAAATCCTAATG 8.8 2.2e-05 -10.725 4.658 6 2 gadB site matrix-scan_2026-04-30.4 R -201 -185 TTTTTCATTGAAAAACA 8.5 2.4e-05 -10.632 4.617 7 1 gadB site matrix-scan_2026-04-30.2 R -199 -183 ATTTTTTCATTGAAAAA 8.5 2.6e-05 -10.544 4.579 8 3 gadB site matrix-scan_2026-04-30.2 D -202 -186 TTGTTTTTCAATGAAAA 8.1 4.6e-05 -9.976 4.333 9 4 gadB site matrix-scan_2026-04-30.4 D -195 -179 TCAATGAAAAAATATTA 7.8 5.8e-05 -9.757 4.237 10 2 gadB site matrix-scan_2026-04-30.4 D -198 -182 TTTTCAATGAAAAAATA 7.5 8.1e-05 -9.416 4.089 11 3 gadB site matrix-scan_2026-04-30.3 R -411 -395 GTGTTGACGGGGCTGTT 7.3 1.0e-04 -9.163 3.979 12 1 slyB limit START_END D -324 -1 . 0 0 0 0 slyB site matrix-scan_2026-04-30.4 R -60 -44 TTAATCATTGAAAAATC 8.4 2.7e-05 -10.504 4.562 1 1 slyB site matrix-scan_2026-04-30.4 R -223 -207 TTATTGATTTGAAGATA 8.3 3.1e-05 -10.375 4.506 2 2 slyB site matrix-scan_2026-04-30.2 R -58 -42 GTTTAATCATTGAAAAA 8.3 3.5e-05 -10.265 4.458 3 1 slyB site matrix-scan_2026-04-30.4 R -191 -175 TCAACCAATTATAAACA 7.9 5.1e-05 -9.888 4.294 4 3 slyB site matrix-scan_2026-04-30.3 D -91 -75 ATGCTTGCGTGGCGTTT 7.6 7.6e-05 -9.486 4.120 5 1 mgrB limit START_END D -209 -1 . 0 0 0 0 mgrB site matrix-scan_2026-04-30.3 D -27 -11 CTGGTTGTCGTGGTGTT 11.2 2.8e-07 -15.076 6.547 1 1 ygdR limit START_END D -188 -1 . 0 0 0 0 ygeN limit START_END D -51 -1 . 0 0 0 0 higB limit START_END D -334 -1 . 0 0 0 0 higB site matrix-scan_2026-04-30.3 R -34 -18 CATCTTTCAATGCTTTT 8.6 2.3e-05 -10.667 4.633 1 1 higB site matrix-scan_2026-04-30.6 R -199 -183 ACAGGGATTTTTTGTTT 8.6 2.4e-05 -10.635 4.619 2 1 higB site matrix-scan_2026-04-30.6 D -159 -143 TTAGCGTTTTTCTACGT 8.1 4.5e-05 -10.013 4.349 3 2 higB site matrix-scan_2026-04-30.6 R -200 -184 CAGGGATTTTTTGTTTT 7.9 5.6e-05 -9.791 4.252 4 3 higB site matrix-scan_2026-04-30.3 R -260 -244 ACGCTTGCCGCGTCTTA 7.4 9.4e-05 -9.269 4.026 5 2 yrbL limit START_END D -264 -1 . 0 0 0 0 yrbL site matrix-scan_2026-04-30.5 R -118 -102 TAAACAAAACCTAAACA 11.4 2.6e-07 -15.182 6.593 1 1 yrbL site matrix-scan_2026-04-30.6 D -115 -99 TTAGGTTTTGTTTAAGT 9.8 4.1e-06 -12.409 5.389 2 1 yrbL site matrix-scan_2026-04-30.5 D -140 -124 TTAAGAAAACCTTAAGA 9.3 1.1e-05 -11.391 4.947 3 2 yrbL site matrix-scan_2026-04-30.5 R -117 -101 TTAAACAAAACCTAAAC 8.1 4.9e-05 -9.914 4.305 4 3 zntA limit START_END D -124 -1 . 0 0 0 0 hdeD limit START_END D -305 -1 . 0 0 0 0 hdeD site matrix-scan_2026-04-30.4 R -194 -178 GTATTGAAATAAAAATA 11.6 6.6e-08 -16.540 7.183 1 1 hdeD site matrix-scan_2026-04-30.2 R -192 -176 TTGTATTGAAATAAAAA 8.8 1.7e-05 -10.981 4.769 2 1 hdeD site matrix-scan_2026-04-30.6 D -199 -183 TCAGATATTTTTATTTC 8.8 1.8e-05 -10.900 4.734 3 1 hdeD site matrix-scan_2026-04-30.6 R -211 -195 TCTGATTTTGATATTTT 8.5 2.7e-05 -10.520 4.569 4 2 hdeD site matrix-scan_2026-04-30.6 D -87 -71 CAGGGGATTTTCTTCTT 8.3 3.5e-05 -10.268 4.459 5 3 gadE limit START_END D -362 -1 . 0 0 0 0 gadA limit START_END D -261 -1 . 0 0 0 0 gadA site matrix-scan_2026-04-30.5 R -152 -136 ATAACAAAATCCTAAGC 11.3 3.2e-07 -14.953 6.494 1 1 gadA site matrix-scan_2026-04-30.6 D -150 -134 TTAGGATTTTGTTATTT 9.8 4.1e-06 -12.409 5.389 2 1 gadA site matrix-scan_2026-04-30.2 D -180 -164 TGTTTATATTATAAAAA 9.4 5.9e-06 -12.046 5.232 3 1 gadA site matrix-scan_2026-04-30.6 D -149 -133 TAGGATTTTGTTATTTA 9.5 6.6e-06 -11.934 5.183 4 2 gadA site matrix-scan_2026-04-30.2 R -180 -164 TTTTTATAATATAAACA 8.5 2.6e-05 -10.544 4.579 5 2 gadA site matrix-scan_2026-04-30.5 R -237 -221 TAAAAATCGCCCAAACA 8.2 4.4e-05 -10.024 4.353 6 2 gadA site matrix-scan_2026-04-30.4 R -228 -212 TTATCGTAATAAAAATC 8.0 4.6e-05 -9.994 4.340 7 1 gadA site matrix-scan_2026-04-30.2 R -226 -210 TATTATCGTAATAAAAA 8.0 5.3e-05 -9.843 4.275 8 3 yhjC limit START_END D -570 -1 . 0 0 0 0 yhjC site matrix-scan_2026-04-30.6 R -312 -296 TTGCCGTTTGTTATTTT 9.3 8.9e-06 -11.628 5.050 1 1 yhjC site matrix-scan_2026-04-30.5 D -119 -103 TAGAAAAAACAATAAAC 8.9 1.9e-05 -10.864 4.718 2 1 yhjC site matrix-scan_2026-04-30.5 D -114 -98 AAAACAATAAACAATGC 8.1 4.9e-05 -9.914 4.305 3 2 yhjC site matrix-scan_2026-04-30.4 D -349 -333 GCATGCAATTAAAAATG 7.7 6.5e-05 -9.642 4.187 4 1 yhjC site matrix-scan_2026-04-30.5 D -107 -91 TAAACAATGCGATATGC 7.7 7.6e-05 -9.491 4.122 5 3 yiaG limit START_END D -484 -1 . 0 0 0 0 yiaG site matrix-scan_2026-04-30.3 D -133 -117 CCGCTGTGTCTGCTTTT 10.5 1.2e-06 -13.644 5.926 1 1 yiaG site matrix-scan_2026-04-30.4 D -58 -42 GTTTTCAATGGAATATA 7.8 5.8e-05 -9.757 4.237 2 1 yiaG site matrix-scan_2026-04-30.5 R -340 -324 TTAACAATGAAACAACA 7.6 8.3e-05 -9.401 4.083 3 1 yidX limit START_END D -328 -1 . 0 0 0 0 yidX site matrix-scan_2026-04-30.3 R -111 -95 CTTCTTTCCCTCCTGTT 10.2 2.1e-06 -13.082 5.681 1 1 yidX site matrix-scan_2026-04-30.3 D -238 -222 GCGTTTGCCGTGCGTGT 9.5 6.5e-06 -11.948 5.189 2 2 yidX site matrix-scan_2026-04-30.5 R -40 -24 TAAAAAATCCCTTAAAA 9.4 9.8e-06 -11.530 5.007 3 1 yidX site matrix-scan_2026-04-30.3 R -130 -114 GCGCCTGATATCCCTTT 7.9 5.4e-05 -9.825 4.267 4 3 yjbJ limit START_END D -166 -1 . 0 0 0 0 yjeT limit START_END D -132 -1 . 0 0 0 0 yjeT site matrix-scan_2026-04-30.3 D -30 -14 GCGCTTGCCCTGGTTTT 12.5 6.1e-09 -18.911 8.213 1 1 yjeT site matrix-scan_2026-04-30.3 R -107 -91 GAGGATGCGGTGGCTTT 8.9 1.5e-05 -11.080 4.812 2 2 mgtA limit START_END D -191 -1 . 0 0 0 0 fecC limit START_END D -51 -1 . 0 0 0 0 ; ; Matrices ; matrix name ncol nrow pseudo Wmin Wmax Wrange ; 1 matrix-scan_2026-04-30.2 17 4 1 -42.700 12.600 55.300 a:0.303 c:0.197 g:0.199 t:0.301 ; 2 matrix-scan_2026-04-30.3 17 4 1 -45.400 14.500 59.900 a:0.303 c:0.197 g:0.199 t:0.301 ; 3 matrix-scan_2026-04-30.4 17 4 1 -42.600 13.000 55.600 a:0.303 c:0.197 g:0.199 t:0.301 ; 4 matrix-scan_2026-04-30.5 17 4 1 -47.800 13.500 61.300 a:0.303 c:0.197 g:0.199 t:0.301 ; 5 matrix-scan_2026-04-30.6 17 4 1 -44.500 14.000 58.500 a:0.303 c:0.197 g:0.199 t:0.301 ; Number of sequences scanned 26 ; Sum of sequence lengths 6543 ; N residues 0 ; Matches per matrix ; matrix name matches scored ; 1 matrix-scan_2026-04-30.2 15 12254 ; 2 matrix-scan_2026-04-30.3 16 12254 ; 3 matrix-scan_2026-04-30.4 17 12254 ; 4 matrix-scan_2026-04-30.5 18 12254 ; 5 matrix-scan_2026-04-30.6 18 12254 ; TOTAL 84 61270 ; Host name rsat ; Job started 2026-04-30.193925 ; Job done 2026-04-30.193935 ; Seconds 10.32 ; user 10.32 ; system 0.02 ; cuser 0.12 ; csystem 0.01