; matrix-scan -v 1 -matrix_format tab -m $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.193924_jSeUd0.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_2026-04-30.193218_GfGu1D.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_2026-04-30.193218_GfGu1D.fasta.fasta.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.193924_jSeUd0.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_2026-04-30.2 R -24 -8 TCAGTAGCTGAACAGGA 8.8 1.8e-05 -10.945 4.753 1 1 insA site matrix-scan_2026-04-30.3 R -87 -71 CATCATACACTAAATCA 8.2 3.9e-05 -10.141 4.404 2 1 insA site matrix-scan_2026-04-30.4 R -75 -59 CCTCAAAAACACCATCA 7.5 8.8e-05 -9.337 4.055 3 1 borD limit START_END D -341 -1 . 0 0 0 0 borD site matrix-scan_2026-04-30.6 D -121 -105 TTGTTTAGGGTTTGTTT 10.4 1.1e-06 -13.704 5.952 1 1 borD site matrix-scan_2026-04-30.3 R -121 -105 AAACAAACCCTAAACAA 10.0 2.6e-06 -12.862 5.586 2 1 borD site matrix-scan_2026-04-30.4 D -244 -228 CCGGACACTCCCGCAGA 9.7 4.8e-06 -12.251 5.321 3 1 borD site matrix-scan_2026-04-30.2 R -322 -306 CCCGGTGCTGACACGGA 9.1 1.2e-05 -11.333 4.922 4 1 ompT limit START_END D -474 -1 . 0 0 0 0 ompT site matrix-scan_2026-04-30.2 D -389 -373 GCAAGCCATTGCGAGGC 11.5 2.4e-07 -15.251 6.623 1 1 ompT site matrix-scan_2026-04-30.2 R -394 -378 GCAATGGCTTGCAAGGC 10.4 1.8e-06 -13.251 5.755 2 2 ompT site matrix-scan_2026-04-30.6 R -263 -247 TTGTGGTGCTTTTATCT 9.3 8.5e-06 -11.680 5.073 3 1 ompT site matrix-scan_2026-04-30.3 D -150 -134 AAACAAAATATAAACAG 9.1 1.2e-05 -11.357 4.932 4 1 ompT site matrix-scan_2026-04-30.3 D -247 -231 AAAGCATAAAAAAACCA 9.0 1.3e-05 -11.225 4.875 5 2 ompT site matrix-scan_2026-04-30.4 D -243 -227 CATAAAAAAACCACACA 8.7 2.1e-05 -10.774 4.679 6 1 ompT site matrix-scan_2026-04-30.6 R -242 -226 CTGTGTGGTTTTTTTAT 8.3 3.4e-05 -10.275 4.462 7 2 ompT site matrix-scan_2026-04-30.2 R -288 -272 GCCATGCCTTTAGAGGC 8.2 3.7e-05 -10.217 4.437 8 3 ompT site matrix-scan_2026-04-30.3 D -161 -145 CATTCAATACTAAACAA 8.2 3.9e-05 -10.141 4.404 9 3 ompT site matrix-scan_2026-04-30.5 R -290 -274 CATGCCTTTAGAGGCAT 7.9 4.6e-05 -9.977 4.333 10 1 ompT site matrix-scan_2026-04-30.3 D -258 -242 AAAGCACCACAAAAGCA 7.5 8.8e-05 -9.333 4.053 11 4 ompT site matrix-scan_2026-04-30.3 D -196 -180 AATTAAACCAAAAACAG 7.5 8.8e-05 -9.333 4.053 12 5 ompT site matrix-scan_2026-04-30.5 D -291 -275 TATGCCTCTAAAGGCAT 7.3 9.0e-05 -9.310 4.043 13 2 ybeF limit START_END D -309 -1 . 0 0 0 0 ybeF site matrix-scan_2026-04-30.2 R -203 -187 GCAAGGCGTGGCACCGC 9.7 5.2e-06 -12.160 5.281 1 1 ybjX limit START_END D -165 -1 . 0 0 0 0 ybjX site matrix-scan_2026-04-30.3 D -117 -101 AAATATCAACAAAACCC 10.0 2.6e-06 -12.862 5.586 1 1 ybjX site matrix-scan_2026-04-30.2 R -138 -122 GAAGTTAATGACCCGGA 8.7 2.0e-05 -10.819 4.699 2 1 ybjX site matrix-scan_2026-04-30.3 D -111 -95 CAACAAAACCCTAAAAT 8.5 2.7e-05 -10.535 4.575 3 2 nudJ limit START_END D -60 -1 . 0 0 0 0 nudJ site matrix-scan_2026-04-30.5 R -32 -16 CACCACGCAAGCAACGG 8.8 1.6e-05 -11.053 4.800 1 1 yncH limit START_END D -126 -1 . 0 0 0 0 yncH site matrix-scan_2026-04-30.3 R -50 -34 AATTAAAAAACATACCA 9.7 4.5e-06 -12.312 5.347 1 1 yncH site matrix-scan_2026-04-30.5 R -22 -6 CACGCTGAATGAAAAGG 8.3 2.9e-05 -10.447 4.537 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_2026-04-30.4 R -371 -355 CATAAAAATAGCGAATA 9.5 6.5e-06 -11.947 5.188 1 1 gadB site matrix-scan_2026-04-30.4 R -390 -374 GCTAAAATCCCCGCCAA 8.9 1.6e-05 -11.059 4.803 2 2 gadB site matrix-scan_2026-04-30.4 D -256 -240 CATAAAAATAACAGCAT 8.2 4.0e-05 -10.139 4.403 3 3 gadB site matrix-scan_2026-04-30.3 D -251 -235 AAATAACAGCATAAAAC 7.6 7.8e-05 -9.454 4.106 4 1 slyB limit START_END D -324 -1 . 0 0 0 0 slyB site matrix-scan_2026-04-30.3 R -197 -181 AATTATAAACAAAACAT 9.2 1.0e-05 -11.506 4.997 1 1 slyB site matrix-scan_2026-04-30.4 R -87 -71 CATGAAACGCCACGCAA 8.4 3.1e-05 -10.397 4.515 2 1 slyB site matrix-scan_2026-04-30.6 D -87 -71 TTGCGTGGCGTTTCATG 8.1 4.5e-05 -10.019 4.351 3 1 mgrB limit START_END D -209 -1 . 0 0 0 0 mgrB site matrix-scan_2026-04-30.4 D -141 -125 CCGAAAAAGCACGAATA 9.6 5.6e-06 -12.087 5.249 1 1 mgrB site matrix-scan_2026-04-30.2 R -20 -4 GCAAGCCAACACCACGA 9.1 1.2e-05 -11.333 4.922 2 1 mgrB site matrix-scan_2026-04-30.6 D -17 -1 TGGTGTTGGCTTGCTTG 8.7 2.1e-05 -10.781 4.682 3 1 mgrB site matrix-scan_2026-04-30.5 D -145 -129 CATTCCGAAAAAGCACG 7.5 7.4e-05 -9.516 4.133 4 1 ygdR limit START_END D -188 -1 . 0 0 0 0 ygdR site matrix-scan_2026-04-30.5 R -179 -163 CCTCCCGCAGGAGAGCG 8.2 3.3e-05 -10.316 4.480 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_2026-04-30.5 R -303 -287 TAGGCCGGATAAGGCGT 11.8 1.5e-07 -15.711 6.823 1 1 higB site matrix-scan_2026-04-30.5 D -269 -253 CAGGCCGGATAAGACGC 11.2 4.5e-07 -14.624 6.351 2 2 higB site matrix-scan_2026-04-30.5 D -322 -306 CCTGCCGGATGCGGCGT 11.1 5.3e-07 -14.444 6.273 3 3 higB site matrix-scan_2026-04-30.2 D -266 -250 GCCGGATAAGACGCGGC 10.0 3.3e-06 -12.621 5.481 4 1 higB site matrix-scan_2026-04-30.6 D -163 -147 TTGTTTAGCGTTTTTCT 9.5 6.2e-06 -11.999 5.211 5 1 higB site matrix-scan_2026-04-30.5 R -278 -262 CCGGCCTGGAGTAACGT 8.7 1.8e-05 -10.927 4.745 6 4 higB site matrix-scan_2026-04-30.2 R -312 -296 TAAGGCGTTTACGCCGC 8.0 4.6e-05 -9.987 4.337 7 2 higB site matrix-scan_2026-04-30.5 R -321 -305 TACGCCGCATCCGGCAG 7.5 7.4e-05 -9.516 4.133 8 5 yrbL limit START_END D -264 -1 . 0 0 0 0 yrbL site matrix-scan_2026-04-30.3 R -119 -103 AAACAAAACCTAAACAA 11.1 2.5e-07 -15.216 6.608 1 1 yrbL site matrix-scan_2026-04-30.6 D -119 -103 TTGTTTAGGTTTTGTTT 9.7 4.5e-06 -12.321 5.351 2 1 zntA limit START_END D -124 -1 . 0 0 0 0 zntA site matrix-scan_2026-04-30.4 D -42 -26 CCTGACAATCACGGCAA 10.9 4.7e-07 -14.565 6.325 1 1 hdeD limit START_END D -305 -1 . 0 0 0 0 hdeD site matrix-scan_2026-04-30.6 D -239 -223 TGGTTTTCTGTATATGT 8.7 2.1e-05 -10.781 4.682 1 1 gadE limit START_END D -362 -1 . 0 0 0 0 gadE site matrix-scan_2026-04-30.6 D -278 -262 TTTTGTTTGCTATTTAC 8.1 4.5e-05 -10.019 4.351 1 1 gadA limit START_END D -261 -1 . 0 0 0 0 gadA site matrix-scan_2026-04-30.4 R -235 -219 AATAAAAATCGCCCAAA 8.8 1.8e-05 -10.908 4.737 1 1 yhjC limit START_END D -570 -1 . 0 0 0 0 yhjC site matrix-scan_2026-04-30.5 R -165 -149 CATGCCGAATGTGGCGA 10.5 1.4e-06 -13.476 5.853 1 1 yhjC site matrix-scan_2026-04-30.6 R -117 -101 TTGTTTATTGTTTTTTC 9.6 5.3e-06 -12.147 5.275 2 1 yhjC site matrix-scan_2026-04-30.4 R -190 -174 CAGGAAAAGGGCGGAAT 9.3 8.8e-06 -11.640 5.055 3 1 yhjC site matrix-scan_2026-04-30.4 D -48 -32 GATAAAATTCACGCAAT 9.0 1.4e-05 -11.196 4.862 4 2 yhjC site matrix-scan_2026-04-30.5 R -187 -171 CAGCAGGAAAAGGGCGG 8.3 2.9e-05 -10.447 4.537 5 2 yhjC site matrix-scan_2026-04-30.2 D -527 -511 GAAGGGTATTACCCGCG 7.8 5.8e-05 -9.763 4.240 6 1 yhjC site matrix-scan_2026-04-30.4 D -22 -6 CATCAAAGTCGCGGAGC 7.8 6.3e-05 -9.668 4.199 7 3 yiaG limit START_END D -484 -1 . 0 0 0 0 yiaG site matrix-scan_2026-04-30.2 D -157 -141 GCCAGAGCATGCCCTGA 11.0 6.2e-07 -14.288 6.205 1 1 yiaG site matrix-scan_2026-04-30.3 R -349 -333 AAACAACAAATTAACCT 9.5 6.2e-06 -11.994 5.209 2 1 yiaG site matrix-scan_2026-04-30.4 D -468 -452 CCCAAAAAAAGCGCACA 8.9 1.6e-05 -11.059 4.803 3 1 yiaG site matrix-scan_2026-04-30.4 D -466 -450 CAAAAAAAGCGCACAAC 8.7 2.1e-05 -10.774 4.679 4 2 yiaG site matrix-scan_2026-04-30.6 R -467 -451 TTGTGCGCTTTTTTTGG 8.0 5.0e-05 -9.900 4.300 5 1 yiaG site matrix-scan_2026-04-30.6 D -313 -297 TGCCGTTGCCTTTTTTG 7.7 7.1e-05 -9.552 4.148 6 2 yiaG site matrix-scan_2026-04-30.6 R -465 -449 CGTTGTGCGCTTTTTTT 7.6 7.9e-05 -9.451 4.105 7 3 yidX limit START_END D -328 -1 . 0 0 0 0 yidX site matrix-scan_2026-04-30.6 D -319 -303 TTGTGCTCTGTATGTTC 9.8 3.7e-06 -12.501 5.429 1 1 yidX site matrix-scan_2026-04-30.4 R -234 -218 CATTACACGCACGGCAA 8.8 1.8e-05 -10.908 4.737 2 1 yidX site matrix-scan_2026-04-30.2 D -121 -105 TCAGGCGCTAAACAGGA 8.7 2.0e-05 -10.819 4.699 3 1 yidX site matrix-scan_2026-04-30.5 R -17 -1 CAGTGGGAATAAACCGG 7.7 5.9e-05 -9.738 4.229 4 1 yidX site matrix-scan_2026-04-30.2 D -284 -268 TCGATGCATAACGCGGC 7.7 6.4e-05 -9.653 4.192 5 2 yjbJ limit START_END D -166 -1 . 0 0 0 0 yjbJ site matrix-scan_2026-04-30.3 D -81 -65 CATTCACAACCTAACGA 8.4 3.0e-05 -10.405 4.519 1 1 yjeT limit START_END D -132 -1 . 0 0 0 0 yjeT site matrix-scan_2026-04-30.2 D -34 -18 GCTGGCGCTTGCCCTGG 8.7 2.0e-05 -10.819 4.699 1 1 yjeT site matrix-scan_2026-04-30.6 D -79 -63 TGGTTTTCTTTTTCTAT 8.6 2.4e-05 -10.647 4.624 2 1 yjeT site matrix-scan_2026-04-30.6 D -85 -69 TGTCGGTGGTTTTCTTT 8.3 3.4e-05 -10.275 4.462 3 2 yjeT site matrix-scan_2026-04-30.6 R -111 -95 ATGCGGTGGCTTTATTG 7.8 6.3e-05 -9.666 4.198 4 3 yjeT site matrix-scan_2026-04-30.2 R -39 -23 GCAAGCGCCAGCCAGAT 7.5 8.0e-05 -9.437 4.098 5 2 mgtA limit START_END D -191 -1 . 0 0 0 0 mgtA site matrix-scan_2026-04-30.5 D -170 -154 CCGGATGCGTAAGGCCG 9.8 4.1e-06 -12.406 5.388 1 1 mgtA site matrix-scan_2026-04-30.5 R -31 -15 AATGGCGAATGAGCCGG 8.7 1.8e-05 -10.927 4.745 2 2 mgtA site matrix-scan_2026-04-30.5 R -111 -95 CAGGCGTGGCGAAGCCT 7.5 7.4e-05 -9.516 4.133 3 3 fecC limit START_END D -51 -1 . 0 0 0 0 fecC site matrix-scan_2026-04-30.4 D -43 -27 GATAAAACACCCGGTGC 8.1 4.5e-05 -10.018 4.351 1 1 ; ; Matrices ; matrix name ncol nrow pseudo Wmin Wmax Wrange ; 1 matrix-scan_2026-04-30.2 17 4 1 -38.600 14.800 53.400 a:0.303 c:0.197 g:0.199 t:0.301 ; 2 matrix-scan_2026-04-30.3 17 4 1 -45.500 13.500 59.000 a:0.303 c:0.197 g:0.199 t:0.301 ; 3 matrix-scan_2026-04-30.4 17 4 1 -40.000 13.900 53.900 a:0.303 c:0.197 g:0.199 t:0.301 ; 4 matrix-scan_2026-04-30.5 17 4 1 -37.100 15.400 52.500 a:0.303 c:0.197 g:0.199 t:0.301 ; 5 matrix-scan_2026-04-30.6 17 4 1 -45.900 13.400 59.300 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 16 12254 ; 2 matrix-scan_2026-04-30.3 15 12254 ; 3 matrix-scan_2026-04-30.4 17 12254 ; 4 matrix-scan_2026-04-30.5 17 12254 ; 5 matrix-scan_2026-04-30.6 17 12254 ; TOTAL 82 61270 ; Host name rsat ; Job started 2026-04-30.193924 ; Job done 2026-04-30.193935 ; Seconds 10.39 ; user 10.39 ; system 0.04 ; cuser 0.11 ; csystem 0.01