; matrix-scan -v 1 -matrix_format tab -m $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.195539_H7UZni.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_2026-04-30.195501_bqDzmp.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_2026-04-30.195501_bqDzmp.fasta.fasta.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.195539_H7UZni.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 borD limit START_END D -341 -1 . 0 0 0 0 borD site matrix-scan_2026-04-30.3 R -120 -104 TAAACAAACCCTAAACA 11.9 8.2e-08 -16.313 7.085 1 1 borD site matrix-scan_2026-04-30.2 D -312 -296 CACCGGGGTGTTGGCAT 11.0 6.6e-07 -14.224 6.177 2 1 borD site matrix-scan_2026-04-30.4 R -37 -21 CCAGCGCAGTAGCGAGT 10.2 2.8e-06 -12.784 5.552 3 1 borD site matrix-scan_2026-04-30.4 D -30 -14 ACTGCGCTGGCCCTGCT 10.0 3.7e-06 -12.518 5.436 4 2 borD site matrix-scan_2026-04-30.2 R -319 -303 CACCCCGGTGCTGACAC 9.3 9.0e-06 -11.620 5.046 5 2 borD site matrix-scan_2026-04-30.3 R -121 -105 AAACAAACCCTAAACAA 9.4 9.1e-06 -11.608 5.041 6 2 borD site matrix-scan_2026-04-30.6 D -270 -254 CCTGTGTGCATCGTTTT 8.4 3.1e-05 -10.369 4.503 7 1 borD site matrix-scan_2026-04-30.6 D -124 -108 TCATTGTTTAGGGTTTG 8.4 3.1e-05 -10.369 4.503 8 2 borD site matrix-scan_2026-04-30.3 D -62 -46 GGAATAACACCATGAAA 7.9 5.6e-05 -9.791 4.252 9 3 borD site matrix-scan_2026-04-30.2 R -77 -61 CCCGATGCTTTTTGAAG 7.6 7.0e-05 -9.570 4.156 10 3 ompT limit START_END D -474 -1 . 0 0 0 0 ompT site matrix-scan_2026-04-30.4 R -444 -428 GCAGAGATGGCGCGGTA 9.0 1.3e-05 -11.214 4.870 1 1 ompT site matrix-scan_2026-04-30.5 D -387 -371 AAGCCATTGCGAGGCCT 8.1 3.8e-05 -10.172 4.417 2 1 ompT site matrix-scan_2026-04-30.3 D -197 -181 TAATTAAACCAAAAACA 8.2 4.1e-05 -10.113 4.392 3 1 ompT site matrix-scan_2026-04-30.3 D -151 -135 TAAACAAAATATAAACA 8.2 4.1e-05 -10.113 4.392 4 2 ompT site matrix-scan_2026-04-30.3 D -253 -237 ACCACAAAAGCATAAAA 7.9 5.6e-05 -9.791 4.252 5 3 ompT site matrix-scan_2026-04-30.3 D -216 -200 AATATGAAACAATAACA 7.8 6.3e-05 -9.673 4.201 6 4 ompT site matrix-scan_2026-04-30.4 R -380 -364 ACACATAAGGCCTCGCA 7.5 7.5e-05 -9.503 4.127 7 2 ompT site matrix-scan_2026-04-30.5 D -29 -13 TAGTCCTGACAACCCCT 7.4 8.3e-05 -9.393 4.079 8 2 ompT site matrix-scan_2026-04-30.3 D -237 -221 AAAACCACACAGTAAAA 7.5 8.6e-05 -9.361 4.066 9 5 ompT site matrix-scan_2026-04-30.6 R -239 -223 TTACTGTGTGGTTTTTT 7.6 8.6e-05 -9.360 4.065 10 1 ybeF limit START_END D -309 -1 . 0 0 0 0 ybeF site matrix-scan_2026-04-30.5 R -205 -189 AAGGCGTGGCACCGCAT 9.4 7.2e-06 -11.848 5.145 1 1 ybeF site matrix-scan_2026-04-30.4 R -198 -182 ACGGAGCAAGGCGTGGC 8.5 2.5e-05 -10.616 4.611 2 1 ybeF site matrix-scan_2026-04-30.4 D -197 -181 CCACGCCTTGCTCCGTA 7.4 8.2e-05 -9.410 4.087 3 2 ybjX limit START_END D -165 -1 . 0 0 0 0 ybjX site matrix-scan_2026-04-30.3 D -112 -96 TCAACAAAACCCTAAAA 8.5 2.8e-05 -10.472 4.548 1 1 nudJ limit START_END D -60 -1 . 0 0 0 0 yncH limit START_END D -126 -1 . 0 0 0 0 gadC limit START_END D -206 -1 . 0 0 0 0 gadC site matrix-scan_2026-04-30.5 R -204 -188 CCGTTACCGTTAAACGT 8.5 2.3e-05 -10.666 4.632 1 1 gadC site matrix-scan_2026-04-30.5 D -196 -180 CGGTAACGGTGTCCCGA 7.5 7.6e-05 -9.491 4.122 2 2 gadC site matrix-scan_2026-04-30.5 D -92 -76 CAGGTGCGGTTCCGACA 7.3 9.3e-05 -9.285 4.032 3 3 gadB limit START_END D -412 -1 . 0 0 0 0 gadB site matrix-scan_2026-04-30.5 D -409 -393 CAGCCCCGTCAACACAT 9.9 3.5e-06 -12.570 5.459 1 1 gadB site matrix-scan_2026-04-30.3 D -252 -236 AAAATAACAGCATAAAA 9.7 6.1e-06 -12.008 5.215 2 1 slyB limit START_END D -324 -1 . 0 0 0 0 mgrB limit START_END D -209 -1 . 0 0 0 0 mgrB site matrix-scan_2026-04-30.3 R -42 -26 AGAACGACCCATCGAAA 7.7 7.0e-05 -9.568 4.155 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_2026-04-30.5 R -278 -262 CCGGCCTGGAGTAACGT 10.1 2.6e-06 -12.860 5.585 1 1 higB site matrix-scan_2026-04-30.4 R -322 -306 ACGCCGCATCCGGCAGG 9.6 6.4e-06 -11.964 5.196 2 1 higB site matrix-scan_2026-04-30.3 R -152 -136 AGAATAAACGTAGAAAA 9.5 7.9e-06 -11.748 5.102 3 1 higB site matrix-scan_2026-04-30.4 D -256 -240 ACGCGGCAAGCGTCGCA 9.4 8.2e-06 -11.717 5.089 4 2 higB site matrix-scan_2026-04-30.3 R -163 -147 AGAAAAACGCTAAACAA 9.3 1.0e-05 -11.474 4.983 5 2 higB site matrix-scan_2026-04-30.4 D -321 -305 CTGCCGGATGCGGCGTA 8.5 2.5e-05 -10.616 4.611 6 3 higB site matrix-scan_2026-04-30.2 R -321 -305 TACGCCGCATCCGGCAG 8.3 3.2e-05 -10.360 4.499 7 1 higB site matrix-scan_2026-04-30.5 D -223 -207 CAGTTCTGGAATCGCGC 8.2 3.4e-05 -10.290 4.469 8 2 higB site matrix-scan_2026-04-30.4 D -265 -249 CCGGATAAGACGCGGCA 7.8 5.4e-05 -9.822 4.266 9 4 yrbL limit START_END D -264 -1 . 0 0 0 0 yrbL site matrix-scan_2026-04-30.3 R -118 -102 TAAACAAAACCTAAACA 11.4 3.2e-07 -14.950 6.493 1 1 yrbL site matrix-scan_2026-04-30.6 D -122 -106 GCATTGTTTAGGTTTTG 9.5 5.2e-06 -12.168 5.285 2 1 yrbL site matrix-scan_2026-04-30.2 R -238 -222 TCGGGGGGAGTTTGAAG 9.4 7.8e-06 -11.756 5.105 3 1 yrbL site matrix-scan_2026-04-30.3 R -119 -103 AAACAAAACCTAAACAA 9.5 7.9e-06 -11.748 5.102 4 2 yrbL site matrix-scan_2026-04-30.2 D -27 -11 CCCCTGGGCACCGGAAG 8.2 3.6e-05 -10.231 4.443 5 2 yrbL site matrix-scan_2026-04-30.2 R -38 -22 CAGGGGACTTTGTTCAG 7.4 8.6e-05 -9.356 4.063 6 3 zntA limit START_END D -124 -1 . 0 0 0 0 zntA site matrix-scan_2026-04-30.4 R -64 -48 ACATGGCATCCTCCGGT 8.1 3.9e-05 -10.150 4.408 1 1 zntA site matrix-scan_2026-04-30.2 D -99 -83 CAGAGTGTATCCTTCGG 7.9 5.0e-05 -9.900 4.300 2 1 zntA site matrix-scan_2026-04-30.4 D -63 -47 CCGGAGGATGCCATGTC 7.4 8.2e-05 -9.410 4.087 3 2 zntA site matrix-scan_2026-04-30.2 R -31 -15 GAGGGGCTTTCTTGCCG 7.3 9.6e-05 -9.252 4.018 4 2 hdeD limit START_END D -305 -1 . 0 0 0 0 hdeD site matrix-scan_2026-04-30.3 R -68 -52 AGAACCACCCTATAAAA 10.0 3.8e-06 -12.473 5.417 1 1 gadE limit START_END D -362 -1 . 0 0 0 0 gadE site matrix-scan_2026-04-30.2 D -17 -1 TACAGGGCTTTTGGCAG 9.9 3.9e-06 -12.464 5.413 1 1 gadA limit START_END D -261 -1 . 0 0 0 0 gadA site matrix-scan_2026-04-30.6 D -162 -146 TCGTTTTTCTGCTTAGG 8.3 3.6e-05 -10.229 4.443 1 1 gadA site matrix-scan_2026-04-30.3 R -187 -171 AATATAAACATTTAACA 7.5 8.6e-05 -9.361 4.066 2 1 yhjC limit START_END D -570 -1 . 0 0 0 0 yhjC site matrix-scan_2026-04-30.6 R -114 -98 GCATTGTTTATTGTTTT 10.1 1.5e-06 -13.390 5.815 1 1 yhjC site matrix-scan_2026-04-30.3 D -118 -102 AGAAAAAACAATAAACA 9.6 7.0e-06 -11.869 5.155 2 1 yhjC site matrix-scan_2026-04-30.2 R -237 -221 CAGAGCGTATTTTTCAG 8.8 1.7e-05 -10.957 4.759 3 1 yhjC site matrix-scan_2026-04-30.6 R -314 -298 GCCGTTTGTTATTTTGG 7.9 6.0e-05 -9.715 4.219 4 2 yiaG limit START_END D -484 -1 . 0 0 0 0 yiaG site matrix-scan_2026-04-30.4 D -156 -140 CCAGAGCATGCCCTGAC 12.2 1.1e-07 -16.065 6.977 1 1 yiaG site matrix-scan_2026-04-30.2 R -144 -128 CAGCGGGGTGAAGTCAG 10.5 1.5e-06 -13.387 5.814 2 1 yiaG site matrix-scan_2026-04-30.6 R -464 -448 TCGTTGTGCGCTTTTTT 9.4 6.3e-06 -11.979 5.202 3 1 yiaG site matrix-scan_2026-04-30.6 D -312 -296 GCCGTTGCCTTTTTTGT 8.7 2.1e-05 -10.785 4.684 4 2 yiaG site matrix-scan_2026-04-30.4 R -37 -21 ACAGCTCATGCATTGGA 8.5 2.5e-05 -10.616 4.611 5 2 yiaG site matrix-scan_2026-04-30.2 D -447 -431 CACACGCGTGTCTGACG 8.4 2.8e-05 -10.479 4.551 6 2 yiaG site matrix-scan_2026-04-30.6 R -466 -450 GTTGTGCGCTTTTTTTG 8.4 3.1e-05 -10.369 4.503 7 3 yidX limit START_END D -328 -1 . 0 0 0 0 yidX site matrix-scan_2026-04-30.6 R -181 -165 GCATTGTTCTTTTTGTG 9.7 3.6e-06 -12.534 5.444 1 1 yidX site matrix-scan_2026-04-30.3 D -174 -158 AGAACAATGCATAAAAA 9.1 1.4e-05 -11.197 4.863 2 1 yidX site matrix-scan_2026-04-30.6 D -322 -306 TCCTTGTGCTCTGTATG 8.6 2.4e-05 -10.638 4.620 3 2 yidX site matrix-scan_2026-04-30.3 R -40 -24 TAAAAAATCCCTTAAAA 8.6 2.5e-05 -10.579 4.594 4 2 yjbJ limit START_END D -166 -1 . 0 0 0 0 yjbJ site matrix-scan_2026-04-30.6 R -47 -31 GCCGGCTTCATCTTTAT 7.8 6.9e-05 -9.583 4.162 1 1 yjeT limit START_END D -132 -1 . 0 0 0 0 yjeT site matrix-scan_2026-04-30.4 R -34 -18 CCAGGGCAAGCGCCAGC 11.9 1.8e-07 -15.525 6.742 1 1 yjeT site matrix-scan_2026-04-30.4 D -33 -17 CTGGCGCTTGCCCTGGT 10.1 3.2e-06 -12.643 5.491 2 2 yjeT site matrix-scan_2026-04-30.6 D -83 -67 TCGGTGGTTTTCTTTTT 9.4 6.3e-06 -11.979 5.202 3 1 yjeT site matrix-scan_2026-04-30.4 R -104 -88 CCTGAGGATGCGGTGGC 9.5 7.2e-06 -11.846 5.145 4 3 yjeT site matrix-scan_2026-04-30.2 D -37 -21 CTGGCTGGCGCTTGCCC 8.4 2.8e-05 -10.479 4.551 5 1 yjeT site matrix-scan_2026-04-30.4 D -103 -87 CCACCGCATCCTCAGGG 8.3 3.1e-05 -10.386 4.511 6 4 yjeT site matrix-scan_2026-04-30.2 D -93 -77 CTCAGGGATGTCGGTGG 7.3 9.6e-05 -9.252 4.018 7 2 mgtA limit START_END D -191 -1 . 0 0 0 0 mgtA site matrix-scan_2026-04-30.5 R -111 -95 CAGGCGTGGCGAAGCCT 11.3 3.3e-07 -14.923 6.481 1 1 mgtA site matrix-scan_2026-04-30.5 D -117 -101 CAGGTAAGGCTTCGCCA 9.8 4.1e-06 -12.407 5.388 2 2 mgtA site matrix-scan_2026-04-30.5 D -112 -96 AAGGCTTCGCCACGCCT 8.8 1.6e-05 -11.032 4.791 3 3 mgtA site matrix-scan_2026-04-30.6 D -140 -124 TCCCTGCTCAGCTTTAT 8.2 4.2e-05 -10.083 4.379 4 1 mgtA site matrix-scan_2026-04-30.2 D -180 -164 CACGGCGTTACCGGATG 8.0 4.5e-05 -10.002 4.344 5 1 mgtA site matrix-scan_2026-04-30.5 D -143 -127 ACGTCCCTGCTCAGCTT 7.9 4.8e-05 -9.950 4.321 6 4 mgtA site matrix-scan_2026-04-30.4 D -31 -15 CCGGCTCATTCGCCATT 7.9 4.8e-05 -9.941 4.317 7 1 mgtA site matrix-scan_2026-04-30.5 R -151 -135 CAGGGACGTTAAAACGT 7.6 6.7e-05 -9.612 4.174 8 5 mgtA site matrix-scan_2026-04-30.5 D -189 -173 CCGTCTTTTCACGGCGT 7.3 9.3e-05 -9.285 4.032 9 6 mgtA site matrix-scan_2026-04-30.5 D -156 -140 CCGTGACGTTTTAACGT 7.2 1.0e-04 -9.168 3.982 10 7 fecC limit START_END D -51 -1 . 0 0 0 0 fecC site matrix-scan_2026-04-30.4 R -35 -19 CCACAGCAGCACCGGGT 10.7 1.3e-06 -13.517 5.870 1 1 fecC site matrix-scan_2026-04-30.2 D -34 -18 CCCGGTGCTGCTGTGGG 8.0 4.5e-05 -10.002 4.344 2 1 ; ; Matrices ; matrix name ncol nrow pseudo Wmin Wmax Wrange ; 1 matrix-scan_2026-04-30.2 17 4 1 -42.600 14.900 57.500 a:0.303 c:0.197 g:0.199 t:0.301 ; 2 matrix-scan_2026-04-30.3 17 4 1 -45.700 13.800 59.500 a:0.303 c:0.197 g:0.199 t:0.301 ; 3 matrix-scan_2026-04-30.4 17 4 1 -38.800 16.000 54.800 a:0.303 c:0.197 g:0.199 t:0.301 ; 4 matrix-scan_2026-04-30.5 17 4 1 -39.100 14.700 53.800 a:0.303 c:0.197 g:0.199 t:0.301 ; 5 matrix-scan_2026-04-30.6 17 4 1 -43.700 13.000 56.700 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 17 12254 ; 2 matrix-scan_2026-04-30.3 20 12254 ; 3 matrix-scan_2026-04-30.4 20 12254 ; 4 matrix-scan_2026-04-30.5 16 12254 ; 5 matrix-scan_2026-04-30.6 15 12254 ; TOTAL 88 61270 ; Host name rsat ; Job started 2026-04-30.195539 ; Job done 2026-04-30.195549 ; Seconds 9.78 ; user 9.78 ; system 0.06 ; cuser 0.1 ; csystem 0.03