; matrix-scan -v 1 -matrix_format tab -m $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.194012_XYH9Ox.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_2026-04-30.193454_C9d6Ap.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_2026-04-30.193454_C9d6Ap.fasta.fasta.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.194012_XYH9Ox.matrix ; Sequence format fasta ; Pseudo counts 1 ; Background model ; Method input ; Markov order 1 ; Strand undef ; Background pseudo-frequency 0.01 ; Residue probabilities ; a 0.30139 ; c 0.20029 ; g 0.20419 ; t 0.29412 ; 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 ompT limit START_END D -474 -1 . 0 0 0 0 ompT site matrix-scan_2026-04-30.5 R -402 -386 TTGCAAGGCTTTACATG 11.5 2.8e-07 -15.088 6.553 1 1 ompT site matrix-scan_2026-04-30.5 D -391 -375 TTGCAAGCCATTGCGAG 11.4 3.4e-07 -14.898 6.470 2 2 ompT site matrix-scan_2026-04-30.5 D -401 -385 ATGTAAAGCCTTGCAAG 10.3 2.4e-06 -12.938 5.619 3 3 ompT site matrix-scan_2026-04-30.2 R -383 -367 CATAAGGCCTCGCAATG 10.1 3.5e-06 -12.570 5.459 4 1 ompT site matrix-scan_2026-04-30.5 R -392 -376 TCGCAATGGCTTGCAAG 10.0 3.8e-06 -12.479 5.420 5 4 ompT site matrix-scan_2026-04-30.5 D -381 -365 TTGCGAGGCCTTATGTG 9.9 4.4e-06 -12.332 5.356 6 5 ompT site matrix-scan_2026-04-30.5 R -471 -455 TTAAAATGTCGTTCTAG 8.6 2.4e-05 -10.619 4.612 7 6 ompT site matrix-scan_2026-04-30.2 D -400 -384 TGTAAAGCCTTGCAAGC 8.2 3.6e-05 -10.231 4.443 8 2 ompT site matrix-scan_2026-04-30.2 D -44 -28 CGAAACTTCTGGGAATA 8.2 3.6e-05 -10.231 4.443 9 3 ompT site matrix-scan_2026-04-30.4 D -193 -177 TAAACCAAAAACAGATA 8.2 3.8e-05 -10.178 4.420 10 1 ompT site matrix-scan_2026-04-30.4 D -248 -232 AAAAGCATAAAAAAACC 7.7 6.6e-05 -9.625 4.180 11 2 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_2026-04-30.6 R -171 -155 GAAATTGTCCCGAAACG 10.9 6.0e-07 -14.330 6.223 1 1 gadC site matrix-scan_2026-04-30.6 D -192 -176 AACGGTGTCCCGAAACG 10.8 7.6e-07 -14.096 6.122 2 2 gadC site matrix-scan_2026-04-30.6 D -205 -189 AACGTTTAACGGTAACG 8.5 2.9e-05 -10.453 4.540 3 3 gadC site matrix-scan_2026-04-30.2 D -90 -74 GGTGCGGTTCCGACAGG 7.8 5.5e-05 -9.800 4.256 4 1 mgrB limit START_END D -209 -1 . 0 0 0 0 mgrB site matrix-scan_2026-04-30.4 R -36 -20 ACAACCAGAACGACCCA 10.2 2.5e-06 -12.909 5.606 1 1 mgrB site matrix-scan_2026-04-30.5 D -40 -24 TCGATGGGTCGTTCTGG 8.4 3.0e-05 -10.399 4.516 2 1 mgrB site matrix-scan_2026-04-30.3 D -173 -157 GCGGCAATATGCGCTGA 8.3 3.4e-05 -10.296 4.471 3 1 ygdR limit START_END D -188 -1 . 0 0 0 0 ygeN limit START_END D -51 -1 . 0 0 0 0 ygeN site matrix-scan_2026-04-30.6 D -22 -6 AAAATCTCCTGCAAATG 7.8 6.5e-05 -9.643 4.188 1 1 higB limit START_END D -334 -1 . 0 0 0 0 higB site matrix-scan_2026-04-30.3 D -319 -303 GCCGGATGCGGCGTAAA 12.8 1.4e-08 -18.086 7.855 1 1 higB site matrix-scan_2026-04-30.3 R -306 -290 GCCGGATAAGGCGTTTA 12.4 4.7e-08 -16.872 7.327 2 2 higB site matrix-scan_2026-04-30.3 R -250 -234 GCCGGATGCGACGCTTG 12.2 8.0e-08 -16.339 7.096 3 3 higB site matrix-scan_2026-04-30.3 R -324 -308 GCCGCATCCGGCAGGTA 12.1 1.0e-07 -16.071 6.979 4 4 higB site matrix-scan_2026-04-30.3 D -266 -250 GCCGGATAAGACGCGGC 11.1 8.0e-07 -14.036 6.096 5 5 higB site matrix-scan_2026-04-30.3 D -254 -238 GCGGCAAGCGTCGCATC 10.6 1.8e-06 -13.215 5.739 6 6 higB site matrix-scan_2026-04-30.3 D -245 -229 GTCGCATCCGGCAATGT 9.8 5.7e-06 -12.068 5.241 7 7 higB site matrix-scan_2026-04-30.4 D -201 -185 TAAAACAAAAAATCCCT 9.6 6.2e-06 -11.984 5.205 8 1 higB site matrix-scan_2026-04-30.3 D -301 -285 GCCTTATCCGGCCTACG 9.7 6.5e-06 -11.937 5.184 9 8 higB site matrix-scan_2026-04-30.3 R -271 -255 GTCTTATCCGGCCTGGA 9.0 1.5e-05 -11.083 4.813 10 9 higB site matrix-scan_2026-04-30.2 D -277 -261 CGTTACTCCAGGCCGGA 8.9 1.6e-05 -11.044 4.796 11 1 higB site matrix-scan_2026-04-30.5 D -37 -21 TCAAAAAGCATTGAAAG 8.0 4.8e-05 -9.942 4.318 12 1 higB site matrix-scan_2026-04-30.4 D -200 -184 AAAACAAAAAATCCCTG 7.7 6.6e-05 -9.625 4.180 13 2 higB site matrix-scan_2026-04-30.2 D -226 -210 GCCCAGTTCTGGAATCG 7.6 6.8e-05 -9.601 4.170 14 2 yrbL limit START_END D -264 -1 . 0 0 0 0 yrbL site matrix-scan_2026-04-30.4 D -222 -206 ACAATAAGAAAATCACG 10.4 1.8e-06 -13.255 5.757 1 1 yrbL site matrix-scan_2026-04-30.5 R -249 -233 TTGAAGGGAGTTGTATG 9.1 1.3e-05 -11.229 4.877 2 1 yrbL site matrix-scan_2026-04-30.6 D -83 -67 GAGATCGTCAGAAAATA 9.1 1.3e-05 -11.218 4.872 3 1 yrbL site matrix-scan_2026-04-30.6 D -70 -54 AATATTTCCAGGAGATG 8.7 2.3e-05 -10.688 4.642 4 2 yrbL site matrix-scan_2026-04-30.6 R -196 -180 GACGTTGATTGAGAACG 8.6 2.6e-05 -10.564 4.588 5 3 yrbL site matrix-scan_2026-04-30.2 R -68 -52 GCCATCTCCTGGAAATA 8.4 2.9e-05 -10.464 4.545 6 1 hdeD limit START_END D -305 -1 . 0 0 0 0 hdeD site matrix-scan_2026-04-30.4 R -85 -69 TTAAGAAGAAAATCCCC 10.8 8.6e-07 -13.971 6.067 1 1 hdeD site matrix-scan_2026-04-30.6 R -238 -222 GACATATACAGAAAACC 9.4 8.6e-06 -11.659 5.064 2 1 hdeD site matrix-scan_2026-04-30.4 D -289 -273 ATAAAGTGAAAGAGCCG 9.2 1.1e-05 -11.423 4.961 3 2 hdeD site matrix-scan_2026-04-30.6 R -109 -93 AATCTATGCCAAAAACG 8.4 3.3e-05 -10.333 4.488 4 2 hdeD site matrix-scan_2026-04-30.6 R -121 -105 AAACGCGTCTAAGAATG 8.3 3.7e-05 -10.215 4.436 5 3 gadE limit START_END D -362 -1 . 0 0 0 0 yiaG limit START_END D -484 -1 . 0 0 0 0 yiaG site matrix-scan_2026-04-30.2 D -424 -408 GGATAGTCCAGGACAGG 11.9 2.0e-07 -15.405 6.690 1 1 yiaG site matrix-scan_2026-04-30.4 R -133 -117 AAAAGCAGACACAGCGG 10.1 2.9e-06 -12.748 5.537 2 1 yiaG site matrix-scan_2026-04-30.5 R -417 -401 CTGCAAGCCTGTCCTGG 9.4 8.9e-06 -11.631 5.051 3 1 yiaG site matrix-scan_2026-04-30.2 R -150 -134 GGTGAAGTCAGGGCATG 9.3 9.8e-06 -11.534 5.009 4 2 yiaG site matrix-scan_2026-04-30.2 R -161 -145 GGCATGCTCTGGCTATG 9.0 1.4e-05 -11.164 4.849 5 3 yiaG site matrix-scan_2026-04-30.4 D -325 -309 AAAAAATGATAGTGCCG 8.8 1.8e-05 -10.900 4.734 6 2 yjbJ limit START_END D -166 -1 . 0 0 0 0 yjbJ site matrix-scan_2026-04-30.5 R -81 -65 TCGTTAGGTTGTGAATG 9.0 1.5e-05 -11.115 4.827 1 1 yjeT limit START_END D -132 -1 . 0 0 0 0 yjeT site matrix-scan_2026-04-30.4 R -81 -65 AGAAAAAGAAAACCACC 9.3 9.4e-06 -11.572 5.026 1 1 yjeT site matrix-scan_2026-04-30.2 R -38 -22 GGCAAGCGCCAGCCAGA 7.8 5.5e-05 -9.800 4.256 2 1 mgtA limit START_END D -191 -1 . 0 0 0 0 mgtA site matrix-scan_2026-04-30.2 D -115 -99 GGTAAGGCTTCGCCACG 11.5 4.1e-07 -14.716 6.391 1 1 mgtA site matrix-scan_2026-04-30.6 R -188 -172 AACGCCGTGAAAAGACG 10.0 3.3e-06 -12.609 5.476 2 1 mgtA site matrix-scan_2026-04-30.2 R -185 -169 GGTAACGCCGTGAAAAG 10.0 3.9e-06 -12.448 5.406 3 2 mgtA site matrix-scan_2026-04-30.6 R -90 -74 GAAACAGTACAGAAATG 9.2 1.2e-05 -11.358 4.933 4 2 mgtA site matrix-scan_2026-04-30.6 R -142 -126 AAAGCTGAGCAGGGACG 8.7 2.3e-05 -10.688 4.642 5 3 mgtA site matrix-scan_2026-04-30.2 D -110 -94 GGCTTCGCCACGCCTGA 7.4 8.3e-05 -9.397 4.081 6 3 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 -36.800 15.500 52.300 a:0.301 c:0.200 g:0.204 t:0.294 ; 2 matrix-scan_2026-04-30.3 17 4 1 -32.400 14.500 46.900 a:0.301 c:0.200 g:0.204 t:0.294 ; 3 matrix-scan_2026-04-30.4 17 4 1 -36.600 14.200 50.800 a:0.301 c:0.200 g:0.204 t:0.294 ; 4 matrix-scan_2026-04-30.5 17 4 1 -39.500 14.500 54.000 a:0.301 c:0.200 g:0.204 t:0.294 ; 5 matrix-scan_2026-04-30.6 17 4 1 -40.700 13.600 54.300 a:0.301 c:0.200 g:0.204 t:0.294 ; Number of sequences scanned 15 ; Sum of sequence lengths 3543 ; N residues 0 ; Matches per matrix ; matrix name matches scored ; 1 matrix-scan_2026-04-30.2 14 6606 ; 2 matrix-scan_2026-04-30.3 10 6606 ; 3 matrix-scan_2026-04-30.4 11 6606 ; 4 matrix-scan_2026-04-30.5 11 6606 ; 5 matrix-scan_2026-04-30.6 13 6606 ; TOTAL 59 33030 ; Host name rsat ; Job started 2026-04-30.194012 ; Job done 2026-04-30.194019 ; Seconds 7.35 ; user 7.35 ; system 0.04 ; cuser 0.1 ; csystem 0.02