; matrix-scan -v 1 -matrix_format tab -m $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.195920_0YKGzI.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_2026-04-30.195733_BWJu75.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_2026-04-30.195733_BWJu75.fasta.fasta.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.195920_0YKGzI.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_2026-04-30.6 D -97 -81 GCCAACTTACTGATTTA 9.1 1.3e-05 -11.256 4.888 1 1 insA site matrix-scan_2026-04-30.5 D -53 -37 CAGTGGCTTCTGTTTCT 8.0 5.3e-05 -9.848 4.277 2 1 borD limit START_END D -341 -1 . 0 0 0 0 borD site matrix-scan_2026-04-30.2 D -122 -106 ATTGTTTAGGGTTTGTT 11.0 7.5e-07 -14.105 6.126 1 1 borD site matrix-scan_2026-04-30.5 D -113 -97 GGTTTGTTTAATTTTCT 10.4 1.4e-06 -13.509 5.867 2 1 borD site matrix-scan_2026-04-30.4 R -323 -307 CCGGTGCTGACACGGAA 10.2 2.2e-06 -13.020 5.654 3 1 borD site matrix-scan_2026-04-30.4 R -223 -207 ACAGCCCTGACGGGGAA 9.6 5.5e-06 -12.112 5.260 4 2 borD site matrix-scan_2026-04-30.4 R -247 -231 GCGGGAGTGTCCGGGAA 8.7 1.9e-05 -10.895 4.732 5 3 borD site matrix-scan_2026-04-30.3 D -119 -103 GTTTAGGGTTTGTTTAA 7.9 6.0e-05 -9.728 4.225 6 1 borD site matrix-scan_2026-04-30.3 D -115 -99 AGGGTTTGTTTAATTTT 7.8 6.7e-05 -9.606 4.172 7 2 ompT limit START_END D -474 -1 . 0 0 0 0 ompT site matrix-scan_2026-04-30.2 R -149 -133 ACTGTTTATATTTTGTT 11.1 6.3e-07 -14.272 6.198 1 1 ompT site matrix-scan_2026-04-30.4 R -444 -428 GCAGAGATGGCGCGGTA 10.7 9.7e-07 -13.850 6.015 2 1 ompT site matrix-scan_2026-04-30.2 R -195 -179 TCTGTTTTTGGTTTAAT 10.5 1.9e-06 -13.189 5.728 3 2 ompT site matrix-scan_2026-04-30.4 D -287 -271 CCTCTAAAGGCATGGCA 9.9 3.5e-06 -12.570 5.459 4 2 ompT site matrix-scan_2026-04-30.3 R -103 -87 ATGTATTTTTTATATCT 9.6 6.0e-06 -12.027 5.223 5 1 ompT site matrix-scan_2026-04-30.3 R -246 -230 GTGGTTTTTTTATGCTT 9.4 8.1e-06 -11.726 5.092 6 2 ompT site matrix-scan_2026-04-30.3 R -198 -182 GTTTTTGGTTTAATTAT 9.3 9.5e-06 -11.569 5.024 7 3 ompT site matrix-scan_2026-04-30.2 R -160 -144 TTTGTTTAGTATTGAAT 9.2 1.3e-05 -11.266 4.893 8 3 ompT site matrix-scan_2026-04-30.2 R -250 -234 TTTTTTTATGCTTTTGT 8.8 2.1e-05 -10.776 4.680 9 4 ompT site matrix-scan_2026-04-30.3 R -217 -201 GTTATTGTTTCATATTT 8.7 2.3e-05 -10.692 4.644 10 4 ompT site matrix-scan_2026-04-30.5 R -148 -132 CACTGTTTATATTTTGT 8.6 2.5e-05 -10.580 4.595 11 1 ompT site matrix-scan_2026-04-30.3 R -152 -136 GTTTATATTTTGTTTAG 8.2 4.2e-05 -10.067 4.372 12 5 ompT site matrix-scan_2026-04-30.5 R -248 -232 GGTTTTTTTATGCTTTT 7.9 5.9e-05 -9.746 4.232 13 2 ompT site matrix-scan_2026-04-30.5 R -99 -83 GAATATGTATTTTTTAT 7.6 8.2e-05 -9.414 4.088 14 3 ompT site matrix-scan_2026-04-30.4 R -380 -364 ACACATAAGGCCTCGCA 7.3 9.4e-05 -9.275 4.028 15 3 ybeF limit START_END D -309 -1 . 0 0 0 0 ybeF site matrix-scan_2026-04-30.6 R -21 -5 GACGACTTTCTGCTTAA 11.6 2.2e-08 -17.642 7.662 1 1 ybeF site matrix-scan_2026-04-30.5 D -237 -221 GCGTTTGTATATTTTCT 10.7 7.2e-07 -14.139 6.140 2 1 ybeF site matrix-scan_2026-04-30.6 D -196 -180 CACGCCTTGCTCCGTAA 9.4 7.7e-06 -11.770 5.112 3 2 ybeF site matrix-scan_2026-04-30.4 R -204 -188 CAAGGCGTGGCACCGCA 8.7 1.9e-05 -10.895 4.732 4 1 ybeF site matrix-scan_2026-04-30.6 R -44 -28 TTCAATTTGATTATTAC 8.7 2.3e-05 -10.663 4.631 5 3 ybeF site matrix-scan_2026-04-30.4 D -211 -195 GCAGAAATGCGGTGCCA 8.4 2.7e-05 -10.533 4.575 6 2 ybeF site matrix-scan_2026-04-30.4 R -199 -183 CGGAGCAAGGCGTGGCA 8.2 3.4e-05 -10.280 4.464 7 3 ybeF site matrix-scan_2026-04-30.3 D -100 -84 TGTAATTTTTTAAATAT 7.6 8.3e-05 -9.400 4.083 8 1 ybjX limit START_END D -165 -1 . 0 0 0 0 ybjX site matrix-scan_2026-04-30.3 R -117 -101 GGGTTTTGTTGATATTT 9.8 4.3e-06 -12.355 5.366 1 1 nudJ limit START_END D -60 -1 . 0 0 0 0 nudJ site matrix-scan_2026-04-30.4 R -34 -18 CCACGCAAGCAACGGTA 7.9 4.8e-05 -9.940 4.317 1 1 yncH limit START_END D -126 -1 . 0 0 0 0 yncH site matrix-scan_2026-04-30.2 D -47 -31 TATGTTTTTTAATTTAT 8.9 1.8e-05 -10.905 4.736 1 1 yncH site matrix-scan_2026-04-30.3 D -50 -34 TGGTATGTTTTTTAATT 7.4 1.0e-04 -9.193 3.992 2 1 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_2026-04-30.3 D -148 -132 AGGATTTTGTTATTTAA 9.4 8.1e-06 -11.726 5.092 1 1 gadB site matrix-scan_2026-04-30.2 R -255 -239 TATGCTGTTATTTTTAT 7.7 7.1e-05 -9.560 4.152 2 1 slyB limit START_END D -324 -1 . 0 0 0 0 slyB site matrix-scan_2026-04-30.2 D -193 -177 TTTGTTTATAATTGGTT 11.2 5.1e-07 -14.497 6.296 1 1 slyB site matrix-scan_2026-04-30.3 D -201 -185 ATGAATGTTTTGTTTAT 10.2 2.1e-06 -13.070 5.676 2 1 slyB site matrix-scan_2026-04-30.5 R -141 -125 CCATGGTTACATGTTCT 9.5 6.8e-06 -11.894 5.165 3 1 slyB site matrix-scan_2026-04-30.3 D -197 -181 ATGTTTTGTTTATAATT 9.4 8.1e-06 -11.726 5.092 4 2 slyB site matrix-scan_2026-04-30.2 D -157 -141 TTTGCTCATATTTGGTA 7.6 7.7e-05 -9.466 4.111 5 2 mgrB limit START_END D -209 -1 . 0 0 0 0 mgrB site matrix-scan_2026-04-30.2 D -202 -186 TCTTCTCTTTTTATGTT 7.6 7.7e-05 -9.466 4.111 1 1 ygdR limit START_END D -188 -1 . 0 0 0 0 ygdR site matrix-scan_2026-04-30.6 D -132 -116 AAGATTTTCCTGCTTTC 7.8 7.2e-05 -9.539 4.143 1 1 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_2026-04-30.4 D -265 -249 CCGGATAAGACGCGGCA 10.4 1.6e-06 -13.359 5.802 1 1 higB site matrix-scan_2026-04-30.3 R -202 -186 GGGATTTTTTGTTTTAT 9.4 8.1e-06 -11.726 5.092 2 1 higB site matrix-scan_2026-04-30.3 R -201 -185 AGGGATTTTTTGTTTTA 8.2 4.2e-05 -10.067 4.372 3 2 higB site matrix-scan_2026-04-30.4 D -238 -222 CCGGCAATGTCTGCCCA 7.7 6.1e-05 -9.702 4.213 4 2 yrbL limit START_END D -264 -1 . 0 0 0 0 yrbL site matrix-scan_2026-04-30.2 D -120 -104 ATTGTTTAGGTTTTGTT 11.0 7.5e-07 -14.105 6.126 1 1 yrbL site matrix-scan_2026-04-30.5 R -146 -130 GGTTTTCTTAAGGTTCT 10.5 1.1e-06 -13.704 5.951 2 1 yrbL site matrix-scan_2026-04-30.3 D -113 -97 AGGTTTTGTTTAAGTTA 8.9 1.7e-05 -10.977 4.767 3 1 yrbL site matrix-scan_2026-04-30.3 D -117 -101 GTTTAGGTTTTGTTTAA 8.1 4.8e-05 -9.950 4.321 4 2 yrbL site matrix-scan_2026-04-30.5 D -181 -165 TCATTTGTACATTTTGT 7.6 8.2e-05 -9.414 4.088 5 2 yrbL site matrix-scan_2026-04-30.6 D -47 -31 TTCGCTTATCTGAACAA 7.6 8.8e-05 -9.333 4.053 6 1 zntA limit START_END D -124 -1 . 0 0 0 0 zntA site matrix-scan_2026-04-30.6 D -17 -1 CTCAATTTGCTGCGTTC 8.8 2.0e-05 -10.804 4.692 1 1 hdeD limit START_END D -305 -1 . 0 0 0 0 hdeD site matrix-scan_2026-04-30.5 D -61 -45 GGGTGGTTCTATGTTAT 11.3 1.7e-07 -15.609 6.779 1 1 hdeD site matrix-scan_2026-04-30.2 R -211 -195 TCTGATTTTGATATTTT 10.2 3.1e-06 -12.685 5.509 2 1 hdeD site matrix-scan_2026-04-30.2 D -79 -63 TTTCTTCTTAATTTTAT 7.7 7.1e-05 -9.560 4.152 3 2 gadE limit START_END D -362 -1 . 0 0 0 0 gadE site matrix-scan_2026-04-30.5 R -263 -247 GGTTGTTATCAGCTTGT 9.1 1.3e-05 -11.269 4.894 1 1 gadE site matrix-scan_2026-04-30.6 R -212 -196 TTCAGATTTATCCATCA 7.6 8.8e-05 -9.333 4.053 2 1 gadA limit START_END D -261 -1 . 0 0 0 0 gadA site matrix-scan_2026-04-30.2 D -206 -190 TCTGTTTTTAATATTAT 10.7 1.3e-06 -13.527 5.875 1 1 gadA site matrix-scan_2026-04-30.2 D -155 -139 TCTGCTTAGGATTTTGT 10.3 2.6e-06 -12.860 5.585 2 2 gadA site matrix-scan_2026-04-30.6 D -163 -147 GTCGTTTTTCTGCTTAG 9.6 5.5e-06 -12.108 5.258 3 1 gadA site matrix-scan_2026-04-30.3 D -148 -132 AGGATTTTGTTATTTAA 9.4 8.1e-06 -11.726 5.092 4 1 yhjC limit START_END D -570 -1 . 0 0 0 0 yhjC site matrix-scan_2026-04-30.2 R -116 -100 ATTGTTTATTGTTTTTT 10.4 2.2e-06 -13.024 5.656 1 1 yhjC site matrix-scan_2026-04-30.3 R -119 -103 GTTTATTGTTTTTTCTA 9.2 1.1e-05 -11.396 4.949 2 1 yhjC site matrix-scan_2026-04-30.5 R -114 -98 GCATTGTTTATTGTTTT 8.5 2.9e-05 -10.465 4.545 3 1 yhjC site matrix-scan_2026-04-30.6 D -210 -194 TTCACCTTTCTCAGAAA 8.5 3.0e-05 -10.403 4.518 4 1 yhjC site matrix-scan_2026-04-30.5 R -148 -132 GGGTTTCACAATGTTGT 8.4 3.2e-05 -10.341 4.491 5 2 yhjC site matrix-scan_2026-04-30.4 R -189 -173 GCAGGAAAAGGGCGGAA 8.2 3.4e-05 -10.280 4.464 6 1 yhjC site matrix-scan_2026-04-30.2 R -291 -275 TTTGTGCTTATTTTTGT 8.0 5.2e-05 -9.871 4.287 7 2 yhjC site matrix-scan_2026-04-30.5 R -115 -99 CATTGTTTATTGTTTTT 7.6 8.2e-05 -9.414 4.088 8 3 yhjC site matrix-scan_2026-04-30.4 D -23 -7 TCATCAAAGTCGCGGAG 7.4 8.4e-05 -9.383 4.075 9 2 yiaG limit START_END D -484 -1 . 0 0 0 0 yiaG site matrix-scan_2026-04-30.4 R -148 -132 GGGGTGAAGTCAGGGCA 9.1 1.1e-05 -11.416 4.958 1 1 yiaG site matrix-scan_2026-04-30.4 D -417 -401 CCAGGACAGGCTTGCAG 8.5 2.4e-05 -10.656 4.628 2 2 yiaG site matrix-scan_2026-04-30.2 D -342 -326 TTTGTTGTTTCATTGTT 8.5 2.9e-05 -10.435 4.532 3 1 yidX limit START_END D -328 -1 . 0 0 0 0 yidX site matrix-scan_2026-04-30.6 R -57 -41 TTCAACTTCATGATTAA 10.4 9.9e-07 -13.830 6.006 1 1 yidX site matrix-scan_2026-04-30.5 R -164 -148 GCATGTCATTTTTTTAT 8.7 2.2e-05 -10.715 4.653 2 1 yidX site matrix-scan_2026-04-30.2 R -172 -156 TTTTTTTATGCATTGTT 8.7 2.4e-05 -10.655 4.627 3 1 yidX site matrix-scan_2026-04-30.3 R -168 -152 GTCATTTTTTTATGCAT 8.4 3.3e-05 -10.322 4.483 4 1 yidX site matrix-scan_2026-04-30.4 R -233 -217 ACATTACACGCACGGCA 7.7 6.1e-05 -9.702 4.213 5 1 yjbJ limit START_END D -166 -1 . 0 0 0 0 yjbJ site matrix-scan_2026-04-30.6 R -53 -37 TTCATCTTTATTCATAA 10.1 2.0e-06 -13.107 5.692 1 1 yjbJ site matrix-scan_2026-04-30.6 R -106 -90 TTCACTTTTCTTCTGAA 9.8 3.8e-06 -12.486 5.423 2 2 yjbJ site matrix-scan_2026-04-30.6 D -136 -120 GCCAAATTGCTGACTAC 7.5 9.9e-05 -9.217 4.003 3 3 yjbJ site matrix-scan_2026-04-30.2 R -148 -132 TTGGCTTAGGATTATTT 7.3 1.0e-04 -9.169 3.982 4 1 yjeT limit START_END D -132 -1 . 0 0 0 0 yjeT site matrix-scan_2026-04-30.5 D -81 -65 GGTGGTTTTCTTTTTCT 9.8 4.2e-06 -12.372 5.373 1 1 yjeT site matrix-scan_2026-04-30.6 R -57 -41 GTCGAATTCATTCATTA 8.4 3.5e-05 -10.272 4.461 2 1 yjeT site matrix-scan_2026-04-30.4 D -112 -96 TCAATAAAGCCACCGCA 7.5 7.6e-05 -9.480 4.117 3 1 mgtA limit START_END D -191 -1 . 0 0 0 0 mgtA site matrix-scan_2026-04-30.4 R -183 -167 CCGGTAACGCCGTGAAA 8.5 2.4e-05 -10.656 4.628 1 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 -46.200 13.800 60.000 a:0.303 c:0.197 g:0.199 t:0.301 ; 2 matrix-scan_2026-04-30.3 17 4 1 -54.300 13.200 67.500 a:0.303 c:0.197 g:0.199 t:0.301 ; 3 matrix-scan_2026-04-30.4 17 4 1 -34.700 14.500 49.200 a:0.303 c:0.197 g:0.199 t:0.301 ; 4 matrix-scan_2026-04-30.5 17 4 1 -45.600 13.300 58.900 a:0.303 c:0.197 g:0.199 t:0.301 ; 5 matrix-scan_2026-04-30.6 17 4 1 -38.800 12.600 51.400 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 20 12254 ; 2 matrix-scan_2026-04-30.3 20 12254 ; 3 matrix-scan_2026-04-30.4 19 12254 ; 4 matrix-scan_2026-04-30.5 16 12254 ; 5 matrix-scan_2026-04-30.6 15 12254 ; TOTAL 90 61270 ; Host name rsat ; Job started 2026-04-30.195920 ; Job done 2026-04-30.195930 ; Seconds 9.57 ; user 9.57 ; system 0.01 ; cuser 0.1 ; csystem 0