; matrix-scan -v 1 -matrix_format tab -m $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.194013_cQ8AAa.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_2026-04-30.193326_i43Bgt.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_2026-04-30.193326_i43Bgt.fasta.fasta.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.194013_cQ8AAa.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 D -74 -58 GATGGTGTTTTTGAGGT 10.1 2.0e-06 -13.104 5.691 1 1 borD limit START_END D -341 -1 . 0 0 0 0 borD site matrix-scan_2026-04-30.6 D -118 -102 TTTAGGGTTTGTTTAAT 12.1 5.3e-08 -16.749 7.274 1 1 borD site matrix-scan_2026-04-30.3 R -122 -106 AACAAACCCTAAACAAT 10.7 9.7e-07 -13.841 6.011 2 1 borD site matrix-scan_2026-04-30.5 D -119 -103 GTTTAGGGTTTGTTTAA 10.4 2.1e-06 -13.060 5.672 3 1 borD site matrix-scan_2026-04-30.5 R -62 -46 TTTCATGGTGTTATTCC 9.2 1.3e-05 -11.278 4.898 4 2 borD site matrix-scan_2026-04-30.5 D -120 -104 TGTTTAGGGTTTGTTTA 7.4 9.5e-05 -9.263 4.023 5 3 ompT limit START_END D -474 -1 . 0 0 0 0 ompT site matrix-scan_2026-04-30.5 R -237 -221 TTTTACTGTGTGGTTTT 10.5 1.8e-06 -13.225 5.744 1 1 ompT site matrix-scan_2026-04-30.3 D -149 -133 AACAAAATATAAACAGT 9.9 3.9e-06 -12.448 5.406 2 1 ompT site matrix-scan_2026-04-30.5 R -261 -245 TTTTGTGGTGCTTTTAT 8.7 2.3e-05 -10.667 4.633 3 2 ompT site matrix-scan_2026-04-30.5 R -198 -182 GTTTTTGGTTTAATTAT 8.7 2.3e-05 -10.667 4.633 4 3 ompT site matrix-scan_2026-04-30.6 R -243 -227 TGTGTGGTTTTTTTATG 8.7 2.5e-05 -10.601 4.604 5 1 ompT site matrix-scan_2026-04-30.4 R -346 -330 GTTTTTTAGTACAAAAA 8.6 2.6e-05 -10.565 4.588 6 1 ompT site matrix-scan_2026-04-30.6 R -242 -226 CTGTGTGGTTTTTTTAT 7.6 8.0e-05 -9.431 4.096 7 2 ompT site matrix-scan_2026-04-30.3 D -195 -179 ATTAAACCAAAAACAGA 7.5 8.5e-05 -9.377 4.073 8 2 ompT site matrix-scan_2026-04-30.5 R -224 -208 TTTCATATTTCGGTTTT 7.4 9.5e-05 -9.263 4.023 9 4 ompT site matrix-scan_2026-04-30.3 D -262 -246 GATAAAAGCACCACAAA 7.3 1.0e-04 -9.181 3.987 10 3 ybeF limit START_END D -309 -1 . 0 0 0 0 ybeF site matrix-scan_2026-04-30.4 R -81 -65 TTTTATTCATGGAAAAA 10.7 6.8e-07 -14.203 6.168 1 1 ybjX limit START_END D -165 -1 . 0 0 0 0 ybjX site matrix-scan_2026-04-30.6 R -113 -97 TTTAGGGTTTTGTTGAT 10.7 1.3e-06 -13.522 5.873 1 1 ybjX site matrix-scan_2026-04-30.3 D -121 -105 AACGAAATATCAACAAA 9.4 8.3e-06 -11.695 5.079 2 1 ybjX site matrix-scan_2026-04-30.5 R -112 -96 TTTTAGGGTTTTGTTGA 9.5 8.4e-06 -11.689 5.076 3 1 ybjX site matrix-scan_2026-04-30.6 D -75 -59 ATTGATGTTTGGTTAAG 8.9 1.9e-05 -10.852 4.713 4 2 ybjX site matrix-scan_2026-04-30.2 R -115 -99 TAGGGTTTTGTTGATAT 7.6 8.3e-05 -9.395 4.080 5 1 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_2026-04-30.5 D -55 -39 ATTCATGGTATGTTTTT 8.4 3.3e-05 -10.327 4.485 1 1 yncH site matrix-scan_2026-04-30.6 D -51 -35 ATGGTATGTTTTTTAAT 8.0 5.4e-05 -9.828 4.268 2 1 yncH site matrix-scan_2026-04-30.4 R -43 -27 TGATATAAATTAAAAAA 7.9 5.9e-05 -9.741 4.231 3 1 yncH site matrix-scan_2026-04-30.6 D -111 -95 ATTATGTTATTTATTAT 7.7 7.3e-05 -9.521 4.135 4 2 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_2026-04-30.6 D -151 -135 ATTAGGATTTTGTTATT 11.5 2.6e-07 -15.176 6.591 1 1 gadB site matrix-scan_2026-04-30.5 R -252 -236 TTTTATGCTGTTATTTT 11.4 3.6e-07 -14.827 6.439 2 1 gadB site matrix-scan_2026-04-30.4 R -199 -183 ATTTTTTCATTGAAAAA 10.9 3.7e-07 -14.813 6.433 3 1 gadB site matrix-scan_2026-04-30.4 R -144 -128 GTGTTTAAATAACAAAA 10.0 3.0e-06 -12.718 5.523 4 2 gadB site matrix-scan_2026-04-30.5 D -303 -287 TTTTAAGGTCTGATTTT 10.2 3.0e-06 -12.715 5.522 5 2 gadB site matrix-scan_2026-04-30.4 D -201 -185 TGTTTTTCAATGAAAAA 9.8 4.4e-06 -12.345 5.361 6 3 gadB site matrix-scan_2026-04-30.2 R -255 -239 TATGCTGTTATTTTTAT 9.6 5.3e-06 -12.145 5.275 7 1 gadB site matrix-scan_2026-04-30.4 D -200 -184 GTTTTTCAATGAAAAAA 9.6 6.0e-06 -12.016 5.219 8 4 gadB site matrix-scan_2026-04-30.4 R -364 -348 ATTATTACATAAAAATA 9.5 7.0e-06 -11.870 5.155 9 5 gadB site matrix-scan_2026-04-30.2 D -217 -201 GAATTTCATATTGTATT 9.4 7.4e-06 -11.816 5.132 10 2 gadB site matrix-scan_2026-04-30.2 D -146 -130 GATTTTGTTATTTAAAC 8.9 1.6e-05 -11.035 4.792 11 3 gadB site matrix-scan_2026-04-30.5 D -361 -345 TTTTATGTAATAATTTT 8.9 1.8e-05 -10.919 4.742 12 3 gadB site matrix-scan_2026-04-30.2 D -300 -284 TAAGGTCTGATTTTTAC 8.4 3.2e-05 -10.344 4.492 13 4 slyB limit START_END D -324 -1 . 0 0 0 0 slyB site matrix-scan_2026-04-30.4 R -58 -42 GTTTAATCATTGAAAAA 10.0 3.0e-06 -12.718 5.523 1 1 slyB site matrix-scan_2026-04-30.6 D -201 -185 ATGAATGTTTTGTTTAT 9.7 6.8e-06 -11.894 5.165 2 1 slyB site matrix-scan_2026-04-30.3 R -193 -177 AACCAATTATAAACAAA 8.1 4.4e-05 -10.033 4.357 3 1 mgrB limit START_END D -209 -1 . 0 0 0 0 mgrB site matrix-scan_2026-04-30.2 D -33 -17 GTCGTTCTGGTTGTCGT 9.6 5.3e-06 -12.145 5.275 1 1 mgrB site matrix-scan_2026-04-30.3 R -18 -2 AAGCAAGCCAACACCAC 9.2 1.1e-05 -11.402 4.952 2 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_2026-04-30.2 R -204 -188 GATTTTTTGTTTTATGG 7.7 7.5e-05 -9.494 4.123 1 1 yrbL limit START_END D -264 -1 . 0 0 0 0 yrbL site matrix-scan_2026-04-30.3 R -120 -104 AACAAAACCTAAACAAT 11.3 2.6e-07 -15.177 6.591 1 1 yrbL site matrix-scan_2026-04-30.6 D -116 -100 TTTAGGTTTTGTTTAAG 10.6 1.6e-06 -13.323 5.786 2 1 yrbL site matrix-scan_2026-04-30.2 R -225 -209 GATTTTCTTATTGTCGG 9.9 3.0e-06 -12.720 5.524 3 1 yrbL site matrix-scan_2026-04-30.6 R -141 -125 CTTAAGGTTTTCTTAAG 9.8 5.9e-06 -12.036 5.227 4 2 yrbL site matrix-scan_2026-04-30.5 D -117 -101 GTTTAGGTTTTGTTTAA 9.5 8.4e-06 -11.689 5.076 5 1 yrbL site matrix-scan_2026-04-30.2 D -115 -99 TTAGGTTTTGTTTAAGT 8.7 2.2e-05 -10.734 4.662 6 2 yrbL site matrix-scan_2026-04-30.5 D -118 -102 TGTTTAGGTTTTGTTTA 8.3 3.7e-05 -10.210 4.434 7 2 yrbL site matrix-scan_2026-04-30.5 R -140 -124 TCTTAAGGTTTTCTTAA 7.9 5.7e-05 -9.775 4.245 8 3 zntA limit START_END D -124 -1 . 0 0 0 0 zntA site matrix-scan_2026-04-30.6 R -79 -63 GTTAAGTTTTTTCTCAT 9.2 1.3e-05 -11.217 4.872 1 1 hdeD limit START_END D -305 -1 . 0 0 0 0 hdeD site matrix-scan_2026-04-30.5 D -68 -52 TTTTATAGGGTGGTTCT 10.0 4.1e-06 -12.411 5.390 1 1 hdeD site matrix-scan_2026-04-30.6 D -148 -132 ATTAGGAAATTTTTATT 8.9 1.9e-05 -10.852 4.713 2 1 hdeD site matrix-scan_2026-04-30.4 R -194 -178 GTATTGAAATAAAAATA 7.8 6.6e-05 -9.619 4.178 3 1 hdeD site matrix-scan_2026-04-30.2 D -196 -180 GATATTTTTATTTCAAT 7.7 7.5e-05 -9.494 4.123 4 1 gadE limit START_END D -362 -1 . 0 0 0 0 gadE site matrix-scan_2026-04-30.6 D -54 -38 GTTATGATTTTTCTCAT 8.9 1.9e-05 -10.852 4.713 1 1 gadE site matrix-scan_2026-04-30.3 D -261 -245 AAGCTGATAACAACCAG 7.4 9.3e-05 -9.284 4.032 2 1 gadA limit START_END D -261 -1 . 0 0 0 0 gadA site matrix-scan_2026-04-30.6 D -151 -135 CTTAGGATTTTGTTATT 10.8 1.1e-06 -13.693 5.947 1 1 gadA site matrix-scan_2026-04-30.2 D -146 -130 GATTTTGTTATTTAAAT 10.3 1.3e-06 -13.546 5.883 2 1 gadA site matrix-scan_2026-04-30.4 D -181 -165 ATGTTTATATTATAAAA 8.1 4.7e-05 -9.956 4.324 3 1 gadA site matrix-scan_2026-04-30.4 R -225 -209 TTATTATCGTAATAAAA 7.9 5.9e-05 -9.741 4.231 4 2 gadA site matrix-scan_2026-04-30.2 D -91 -75 TACTTTTTTATTGCCTT 7.8 6.7e-05 -9.606 4.172 5 2 yhjC limit START_END D -570 -1 . 0 0 0 0 yhjC site matrix-scan_2026-04-30.5 R -119 -103 GTTTATTGTTTTTTCTA 10.0 4.1e-06 -12.411 5.390 1 1 yhjC site matrix-scan_2026-04-30.6 D -381 -365 TTTGAGGATTTCCTTAT 9.0 1.7e-05 -10.976 4.767 2 1 yhjC site matrix-scan_2026-04-30.3 D -291 -275 ACAAAAATAAGCACAAA 8.1 4.4e-05 -10.033 4.357 3 1 yhjC site matrix-scan_2026-04-30.2 R -343 -327 GAATTTCATTTTTAATT 8.0 5.3e-05 -9.837 4.272 4 1 yhjC site matrix-scan_2026-04-30.2 R -291 -275 TTTGTGCTTATTTTTGT 7.8 6.7e-05 -9.606 4.172 5 2 yhjC site matrix-scan_2026-04-30.3 D -116 -100 AAAAAACAATAAACAAT 7.3 1.0e-04 -9.181 3.987 6 2 yiaG limit START_END D -484 -1 . 0 0 0 0 yiaG site matrix-scan_2026-04-30.3 R -342 -326 AACAATGAAACAACAAA 9.2 1.1e-05 -11.402 4.952 1 1 yiaG site matrix-scan_2026-04-30.3 D -163 -147 ATCATAGCCAGAGCATG 8.3 3.4e-05 -10.275 4.462 2 2 yiaG site matrix-scan_2026-04-30.2 D -345 -329 TAATTTGTTGTTTCATT 7.9 5.9e-05 -9.731 4.226 3 1 yiaG site matrix-scan_2026-04-30.4 D -374 -358 GTAAAATCATGGAGAAA 7.8 6.6e-05 -9.619 4.178 4 1 yiaG site matrix-scan_2026-04-30.4 R -337 -321 TTTTTAACAATGAAACA 7.6 8.2e-05 -9.414 4.088 5 2 yidX limit START_END D -328 -1 . 0 0 0 0 yidX site matrix-scan_2026-04-30.6 D -38 -22 TTAAGGGATTTTTTAAG 10.0 4.4e-06 -12.343 5.360 1 1 yidX site matrix-scan_2026-04-30.5 R -175 -159 TTTTATGCATTGTTCTT 9.3 1.1e-05 -11.424 4.962 2 1 yidX site matrix-scan_2026-04-30.5 D -40 -24 TTTTAAGGGATTTTTTA 9.2 1.3e-05 -11.278 4.898 3 2 yidX site matrix-scan_2026-04-30.3 R -320 -304 AACATACAGAGCACAAG 9.0 1.4e-05 -11.146 4.841 4 1 yidX site matrix-scan_2026-04-30.2 R -183 -167 ATTGTTCTTTTTGTGAT 8.5 2.8e-05 -10.476 4.550 5 1 yidX site matrix-scan_2026-04-30.3 D -183 -167 ATCACAAAAAGAACAAT 7.3 1.0e-04 -9.181 3.987 6 2 yjbJ limit START_END D -166 -1 . 0 0 0 0 yjeT limit START_END D -132 -1 . 0 0 0 0 yjeT site matrix-scan_2026-04-30.3 R -27 -11 ACCAAAACCAGGGCAAG 8.7 2.1e-05 -10.748 4.668 1 1 yjeT site matrix-scan_2026-04-30.6 D -84 -68 GTCGGTGGTTTTCTTTT 8.0 5.4e-05 -9.828 4.268 2 1 yjeT site matrix-scan_2026-04-30.3 D -110 -94 AATAAAGCCACCGCATC 7.7 6.9e-05 -9.589 4.164 3 2 mgtA limit START_END D -191 -1 . 0 0 0 0 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 -44.500 12.400 56.900 a:0.303 c:0.197 g:0.199 t:0.301 ; 2 matrix-scan_2026-04-30.3 17 4 1 -40.000 13.800 53.800 a:0.303 c:0.197 g:0.199 t:0.301 ; 3 matrix-scan_2026-04-30.4 17 4 1 -49.200 13.400 62.600 a:0.303 c:0.197 g:0.199 t:0.301 ; 4 matrix-scan_2026-04-30.5 17 4 1 -44.100 14.000 58.100 a:0.303 c:0.197 g:0.199 t:0.301 ; 5 matrix-scan_2026-04-30.6 17 4 1 -45.800 14.000 59.800 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 17 12254 ; 3 matrix-scan_2026-04-30.4 14 12254 ; 4 matrix-scan_2026-04-30.5 19 12254 ; 5 matrix-scan_2026-04-30.6 18 12254 ; TOTAL 85 61270 ; Host name rsat ; Job started 2026-04-30.194013 ; Job done 2026-04-30.194023 ; Seconds 10.26 ; user 10.26 ; system 0.02 ; cuser 0.11 ; csystem 0.02