; matrix-scan -v 1 -matrix_format tab -m $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.193926_88ea75.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_2026-04-30.193217_wovDZD.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_2026-04-30.193217_wovDZD.fasta.fasta.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.193926_88ea75.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_2026-04-30.4 D -30 -14 TGTCCCTCCTGTTCAGC 10.2 2.0e-06 -13.137 5.705 1 1 borD limit START_END D -341 -1 . 0 0 0 0 borD site matrix-scan_2026-04-30.5 R -117 -101 AATTAAACAAACCCTAA 11.7 6.7e-08 -16.516 7.173 1 1 borD site matrix-scan_2026-04-30.4 R -61 -45 TTTTCATGGTGTTATTC 11.5 1.3e-07 -15.864 6.890 2 1 borD site matrix-scan_2026-04-30.2 D -121 -105 TTGTTTAGGGTTTGTTT 11.2 4.7e-07 -14.581 6.332 3 1 borD site matrix-scan_2026-04-30.2 D -122 -106 ATTGTTTAGGGTTTGTT 10.3 2.6e-06 -12.859 5.585 4 2 borD site matrix-scan_2026-04-30.2 R -60 -44 TTTTTCATGGTGTTATT 10.2 3.1e-06 -12.677 5.506 5 3 borD site matrix-scan_2026-04-30.3 R -123 -107 ACAAACCCTAAACAATG 9.8 4.0e-06 -12.433 5.399 6 1 borD site matrix-scan_2026-04-30.5 R -118 -102 ATTAAACAAACCCTAAA 9.4 8.2e-06 -11.712 5.086 7 2 borD site matrix-scan_2026-04-30.3 R -271 -255 AAACGATGCACACAGGG 9.1 1.2e-05 -11.337 4.924 8 2 borD site matrix-scan_2026-04-30.6 R -312 -296 ATGCCAACACCCCGGTG 9.1 1.2e-05 -11.296 4.906 9 1 borD site matrix-scan_2026-04-30.6 R -335 -319 CGGAAGAAACCGGACGT 8.7 2.1e-05 -10.787 4.685 10 2 borD site matrix-scan_2026-04-30.3 R -269 -253 AAAAACGATGCACACAG 8.5 2.7e-05 -10.528 4.572 11 3 ompT limit START_END D -474 -1 . 0 0 0 0 ompT site matrix-scan_2026-04-30.5 D -153 -137 ACTAAACAAAATATAAA 10.5 1.2e-06 -13.617 5.914 1 1 ompT site matrix-scan_2026-04-30.3 D -259 -243 AAAAGCACCACAAAAGC 10.3 1.6e-06 -13.352 5.799 2 1 ompT site matrix-scan_2026-04-30.3 D -240 -224 AAAAAAACCACACAGTA 10.1 2.4e-06 -12.959 5.628 3 2 ompT site matrix-scan_2026-04-30.3 D -148 -132 ACAAAATATAAACAGTG 9.4 7.5e-06 -11.801 5.125 4 3 ompT site matrix-scan_2026-04-30.2 R -251 -235 TTTTTTATGCTTTTGTG 8.8 2.3e-05 -10.669 4.634 5 1 ompT site matrix-scan_2026-04-30.5 D -243 -227 CATAAAAAAACCACACA 8.6 2.5e-05 -10.594 4.601 6 2 ompT site matrix-scan_2026-04-30.3 R -360 -344 AAAAGAGGGACAAAACT 8.3 3.5e-05 -10.274 4.462 7 4 ybeF limit START_END D -309 -1 . 0 0 0 0 ybeF site matrix-scan_2026-04-30.5 R -232 -216 GATAAAGAAAATATACA 8.8 1.9e-05 -10.853 4.714 1 1 ybjX limit START_END D -165 -1 . 0 0 0 0 ybjX site matrix-scan_2026-04-30.2 R -110 -94 AATTTTAGGGTTTTGTT 11.3 3.5e-07 -14.862 6.455 1 1 ybjX site matrix-scan_2026-04-30.5 D -114 -98 TATCAACAAAACCCTAA 10.5 1.2e-06 -13.617 5.914 2 1 ybjX site matrix-scan_2026-04-30.5 R -74 -58 TCTTAACCAAACATCAA 8.7 2.2e-05 -10.725 4.658 3 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_2026-04-30.2 D -57 -41 AAATTCATGGTATGTTT 8.4 3.6e-05 -10.231 4.443 1 1 gadC limit START_END D -206 -1 . 0 0 0 0 gadC site matrix-scan_2026-04-30.6 R -91 -75 CTGTCGGAACCGCACCT 7.3 9.9e-05 -9.223 4.006 1 1 gadB limit START_END D -412 -1 . 0 0 0 0 gadB site matrix-scan_2026-04-30.5 R -150 -134 AAATAACAAAATCCTAA 10.6 1.0e-06 -13.793 5.990 1 1 gadB site matrix-scan_2026-04-30.2 D -305 -289 TATTTTAAGGTCTGATT 9.9 5.0e-06 -12.209 5.302 2 1 gadB site matrix-scan_2026-04-30.2 R -250 -234 TGTTTTATGCTGTTATT 9.1 1.6e-05 -11.038 4.794 3 2 gadB site matrix-scan_2026-04-30.2 R -264 -248 ATTTTTATGCGCATTCT 8.9 2.0e-05 -10.799 4.690 4 3 gadB site matrix-scan_2026-04-30.3 D -275 -259 TCAGGAGACACAGAATG 8.7 2.1e-05 -10.778 4.681 5 1 gadB site matrix-scan_2026-04-30.3 R -211 -195 AAAAACAATACAATATG 7.6 7.8e-05 -9.457 4.107 6 2 gadB site matrix-scan_2026-04-30.5 D -328 -312 TAATAATCAAGTACTAA 7.6 7.9e-05 -9.450 4.104 7 2 slyB limit START_END D -324 -1 . 0 0 0 0 slyB site matrix-scan_2026-04-30.5 R -200 -184 TATAAACAAAACATTCA 9.9 3.7e-06 -12.501 5.429 1 1 slyB site matrix-scan_2026-04-30.4 R -80 -64 TGTTCACCATGAAACGC 7.8 6.0e-05 -9.724 4.223 2 1 mgrB limit START_END D -209 -1 . 0 0 0 0 mgrB site matrix-scan_2026-04-30.2 D -119 -103 ATAGTTAGGCGCTGTTT 10.8 1.1e-06 -13.728 5.962 1 1 mgrB site matrix-scan_2026-04-30.6 D -144 -128 ATTCCGAAAAAGCACGA 8.2 3.8e-05 -10.191 4.426 2 1 ygdR limit START_END D -188 -1 . 0 0 0 0 ygdR site matrix-scan_2026-04-30.4 R -61 -45 TTTTCATCCGGTTATCC 11.2 2.7e-07 -15.133 6.572 1 1 ygdR site matrix-scan_2026-04-30.2 R -60 -44 TTTTTCATCCGGTTATC 8.1 5.0e-05 -9.902 4.300 2 1 ygdR site matrix-scan_2026-04-30.4 D -128 -112 TTTTCCTGCTTTCAAGA 7.5 8.4e-05 -9.385 4.076 3 2 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_2026-04-30.6 D -321 -305 CTGCCGGATGCGGCGTA 11.3 3.6e-07 -14.836 6.443 1 1 higB site matrix-scan_2026-04-30.3 R -165 -149 AAAAACGCTAAACAAGA 10.2 1.9e-06 -13.148 5.710 2 1 higB site matrix-scan_2026-04-30.6 R -304 -288 AGGCCGGATAAGGCGTT 9.4 8.2e-06 -11.714 5.087 3 2 higB site matrix-scan_2026-04-30.6 R -322 -306 ACGCCGCATCCGGCAGG 9.3 9.4e-06 -11.576 5.027 4 3 higB site matrix-scan_2026-04-30.2 D -163 -147 TTGTTTAGCGTTTTTCT 8.8 2.3e-05 -10.669 4.634 5 1 higB site matrix-scan_2026-04-30.2 D -164 -148 CTTGTTTAGCGTTTTTC 8.7 2.6e-05 -10.555 4.584 6 2 yrbL limit START_END D -264 -1 . 0 0 0 0 yrbL site matrix-scan_2026-04-30.5 D -142 -126 CCTTAAGAAAACCTTAA 11.9 3.4e-08 -17.198 7.469 1 1 yrbL site matrix-scan_2026-04-30.5 R -115 -99 ACTTAAACAAAACCTAA 10.5 1.2e-06 -13.617 5.914 2 2 yrbL site matrix-scan_2026-04-30.2 D -120 -104 ATTGTTTAGGTTTTGTT 10.0 4.3e-06 -12.368 5.371 3 1 yrbL site matrix-scan_2026-04-30.5 R -116 -100 CTTAAACAAAACCTAAA 9.8 4.4e-06 -12.326 5.353 4 3 yrbL site matrix-scan_2026-04-30.3 R -121 -105 ACAAAACCTAAACAATG 9.2 1.0e-05 -11.483 4.987 5 1 yrbL site matrix-scan_2026-04-30.2 D -172 -156 CATTTTGTGCGCTTTTC 8.4 3.6e-05 -10.231 4.443 6 2 yrbL site matrix-scan_2026-04-30.2 D -119 -103 TTGTTTAGGTTTTGTTT 8.4 3.6e-05 -10.231 4.443 7 3 yrbL site matrix-scan_2026-04-30.2 R -234 -218 ATTGTCGGGGGGAGTTT 8.2 4.5e-05 -10.008 4.346 8 4 yrbL site matrix-scan_2026-04-30.3 R -181 -165 ACAAAATGTACAAATGA 8.0 5.0e-05 -9.900 4.300 9 2 zntA limit START_END D -124 -1 . 0 0 0 0 zntA site matrix-scan_2026-04-30.2 R -26 -10 AAATTGAGGGGCTTTCT 7.5 9.1e-05 -9.302 4.040 1 1 hdeD limit START_END D -305 -1 . 0 0 0 0 hdeD site matrix-scan_2026-04-30.4 D -67 -51 TTTATAGGGTGGTTCTA 8.3 3.2e-05 -10.336 4.489 1 1 hdeD site matrix-scan_2026-04-30.2 D -70 -54 AATTTTATAGGGTGGTT 8.3 4.0e-05 -10.124 4.397 2 1 hdeD site matrix-scan_2026-04-30.6 R -87 -71 AAGAAGAAAATCCCCTG 7.7 6.5e-05 -9.633 4.184 3 1 gadE limit START_END D -362 -1 . 0 0 0 0 gadE site matrix-scan_2026-04-30.4 R -117 -101 TTTACATCCTTGTCCGA 9.6 5.3e-06 -12.140 5.272 1 1 gadE site matrix-scan_2026-04-30.4 D -266 -250 TTTACAAGCTGATAACA 9.0 1.3e-05 -11.263 4.891 2 2 gadE site matrix-scan_2026-04-30.6 R -17 -1 CTGCCAAAAGCCCTGTA 7.7 6.5e-05 -9.633 4.184 3 1 gadA limit START_END D -261 -1 . 0 0 0 0 gadA site matrix-scan_2026-04-30.5 R -150 -134 AAATAACAAAATCCTAA 10.6 1.0e-06 -13.793 5.990 1 1 gadA site matrix-scan_2026-04-30.2 D -238 -222 ATGTTTGGGCGATTTTT 9.3 1.2e-05 -11.313 4.913 2 1 gadA site matrix-scan_2026-04-30.6 R -165 -149 AAGCAGAAAAACGACTT 7.6 7.2e-05 -9.537 4.142 3 1 yhjC limit START_END D -570 -1 . 0 0 0 0 yhjC site matrix-scan_2026-04-30.3 D -115 -99 AAAAACAATAAACAATG 9.7 4.7e-06 -12.268 5.328 1 1 yhjC site matrix-scan_2026-04-30.5 R -379 -363 ATATAAGGAAATCCTCA 9.6 6.2e-06 -11.999 5.211 2 1 yhjC site matrix-scan_2026-04-30.4 R -521 -505 TTTTCTCGCGGGTAATA 9.3 8.3e-06 -11.696 5.080 3 1 yhjC site matrix-scan_2026-04-30.6 R -187 -171 CAGCAGGAAAAGGGCGG 9.0 1.4e-05 -11.179 4.855 4 1 yhjC site matrix-scan_2026-04-30.6 R -166 -150 ATGCCGAATGTGGCGAT 8.0 4.7e-05 -9.963 4.327 5 2 yhjC site matrix-scan_2026-04-30.2 R -288 -272 CTATTTGTGCTTATTTT 7.4 9.9e-05 -9.216 4.003 6 1 yiaG limit START_END D -484 -1 . 0 0 0 0 yiaG site matrix-scan_2026-04-30.6 R -135 -119 AAGCAGACACAGCGGGG 10.7 1.1e-06 -13.702 5.951 1 1 yiaG site matrix-scan_2026-04-30.3 D -465 -449 AAAAAAAGCGCACAACG 9.7 4.7e-06 -12.268 5.328 2 1 yiaG site matrix-scan_2026-04-30.6 D -454 -438 ACAACGACACACGCGTG 9.1 1.2e-05 -11.296 4.906 3 2 yiaG site matrix-scan_2026-04-30.4 R -376 -360 TCTCCATGATTTTACCA 8.2 3.7e-05 -10.201 4.430 4 1 yiaG site matrix-scan_2026-04-30.4 R -373 -357 TTTTCTCCATGATTTTA 8.2 3.7e-05 -10.201 4.430 5 2 yidX limit START_END D -328 -1 . 0 0 0 0 yidX site matrix-scan_2026-04-30.4 R -115 -99 TTTCCCTCCTGTTTAGC 11.0 4.0e-07 -14.722 6.394 1 1 yidX site matrix-scan_2026-04-30.3 R -321 -305 ACATACAGAGCACAAGG 9.9 3.3e-06 -12.625 5.483 2 1 yidX site matrix-scan_2026-04-30.2 D -42 -26 AATTTTAAGGGATTTTT 10.1 3.7e-06 -12.513 5.434 3 1 yidX site matrix-scan_2026-04-30.4 R -260 -244 TCATCACGCTGGTACTA 9.7 4.6e-06 -12.296 5.340 4 2 yidX site matrix-scan_2026-04-30.5 R -37 -21 CCTTAAAAAATCCCTTA 9.3 9.5e-06 -11.566 5.023 5 1 yidX site matrix-scan_2026-04-30.3 D -110 -94 ACAGGAGGGAAAGAAGA 9.2 1.0e-05 -11.483 4.987 6 2 yidX site matrix-scan_2026-04-30.3 D -121 -105 TCAGGCGCTAAACAGGA 8.1 4.5e-05 -10.018 4.351 7 3 yidX site matrix-scan_2026-04-30.4 R -126 -110 TTTAGCGCCTGATATCC 7.9 5.3e-05 -9.853 4.279 8 3 yjbJ limit START_END D -166 -1 . 0 0 0 0 yjbJ site matrix-scan_2026-04-30.6 D -44 -28 AAGATGAAGCCGGCGGT 7.3 9.9e-05 -9.223 4.006 1 1 yjeT limit START_END D -132 -1 . 0 0 0 0 yjeT site matrix-scan_2026-04-30.6 D -103 -87 CCACCGCATCCTCAGGG 8.2 3.8e-05 -10.191 4.426 1 1 mgtA limit START_END D -191 -1 . 0 0 0 0 mgtA site matrix-scan_2026-04-30.6 R -32 -16 ATGGCGAATGAGCCGGG 9.8 4.7e-06 -12.267 5.327 1 1 mgtA site matrix-scan_2026-04-30.6 R -180 -164 CATCCGGTAACGCCGTG 9.0 1.4e-05 -11.179 4.855 2 2 mgtA site matrix-scan_2026-04-30.4 D -184 -168 TTTTCACGGCGTTACCG 8.3 3.2e-05 -10.336 4.489 3 1 mgtA site matrix-scan_2026-04-30.5 R -64 -48 ACATAAGGAGTCCCTCC 7.4 9.7e-05 -9.240 4.013 4 1 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 -46.900 13.600 60.500 a:0.303 c:0.197 g:0.199 t:0.301 ; 2 matrix-scan_2026-04-30.3 17 4 1 -40.700 13.400 54.100 a:0.303 c:0.197 g:0.199 t:0.301 ; 3 matrix-scan_2026-04-30.4 17 4 1 -48.400 13.400 61.800 a:0.303 c:0.197 g:0.199 t:0.301 ; 4 matrix-scan_2026-04-30.5 17 4 1 -48.500 13.300 61.800 a:0.303 c:0.197 g:0.199 t:0.301 ; 5 matrix-scan_2026-04-30.6 17 4 1 -42.500 14.500 57.000 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 22 12254 ; 2 matrix-scan_2026-04-30.3 17 12254 ; 3 matrix-scan_2026-04-30.4 15 12254 ; 4 matrix-scan_2026-04-30.5 17 12254 ; 5 matrix-scan_2026-04-30.6 18 12254 ; TOTAL 89 61270 ; Host name rsat ; Job started 2026-04-30.193927 ; Job done 2026-04-30.193938 ; Seconds 11.68 ; user 11.68 ; system 0.04 ; cuser 0.12 ; csystem 0.01