; matrix-scan -v 1 -matrix_format tab -m $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.193922_2nDeXG.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_2026-04-30.193216_7r4C3T.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_2026-04-30.193216_7r4C3T.fasta.fasta.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.193922_2nDeXG.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 -69 -53 TGTTTTTGAGGTGCTCC 9.9 4.0e-06 -12.432 5.399 1 1 insA site matrix-scan_2026-04-30.4 D -80 -64 GTGTATGATGGTGTTTT 8.7 2.4e-05 -10.631 4.617 2 1 borD limit START_END D -341 -1 . 0 0 0 0 borD site matrix-scan_2026-04-30.5 R -121 -105 AAACAAACCCTAAACAA 11.0 2.7e-07 -15.123 6.568 1 1 borD site matrix-scan_2026-04-30.4 R -59 -43 TTTTTTCATGGTGTTAT 10.7 5.3e-07 -14.456 6.278 2 1 borD site matrix-scan_2026-04-30.2 R -61 -45 TTTTCATGGTGTTATTC 8.7 2.2e-05 -10.706 4.650 3 1 borD site matrix-scan_2026-04-30.3 D -150 -134 AAATATTAACAATATGA 8.6 2.7e-05 -10.506 4.563 4 1 borD site matrix-scan_2026-04-30.6 D -320 -304 CGTGTCAGCACCGGGGT 8.1 3.6e-05 -10.239 4.447 5 1 borD site matrix-scan_2026-04-30.2 D -111 -95 TTTGTTTAATTTTCTAC 8.3 3.6e-05 -10.229 4.442 6 2 borD site matrix-scan_2026-04-30.2 D -120 -104 TGTTTAGGGTTTGTTTA 8.2 4.1e-05 -10.100 4.386 7 3 ompT limit START_END D -474 -1 . 0 0 0 0 ompT site matrix-scan_2026-04-30.3 D -156 -140 AATACTAAACAAAATAT 11.2 2.6e-07 -15.162 6.585 1 1 ompT site matrix-scan_2026-04-30.6 D -441 -425 CGCGCCATCTCTGCGCT 10.9 4.4e-07 -14.644 6.360 2 1 ompT site matrix-scan_2026-04-30.5 D -240 -224 AAAAAAACCACACAGTA 10.7 5.9e-07 -14.346 6.230 3 1 ompT site matrix-scan_2026-04-30.3 D -247 -231 AAAGCATAAAAAAACCA 9.6 7.1e-06 -11.859 5.150 4 2 ompT site matrix-scan_2026-04-30.4 R -261 -245 TTTTGTGGTGCTTTTAT 9.2 1.2e-05 -11.366 4.936 5 1 ompT site matrix-scan_2026-04-30.4 R -250 -234 TTTTTTTATGCTTTTGT 9.2 1.2e-05 -11.366 4.936 6 2 ompT site matrix-scan_2026-04-30.2 R -151 -135 TGTTTATATTTTGTTTA 9.2 1.2e-05 -11.363 4.935 7 1 ompT site matrix-scan_2026-04-30.4 D -358 -342 TTTTGTCCCTCTTTTTT 9.0 1.5e-05 -11.077 4.811 8 3 ompT site matrix-scan_2026-04-30.5 D -261 -245 ATAAAAGCACCACAAAA 8.5 2.7e-05 -10.537 4.576 9 2 ompT site matrix-scan_2026-04-30.2 R -197 -181 TGTTTTTGGTTTAATTA 8.3 3.6e-05 -10.229 4.442 10 2 ompT site matrix-scan_2026-04-30.3 D -339 -323 ACTAAAAAACATAGTAA 8.1 4.9e-05 -9.926 4.311 11 3 ompT site matrix-scan_2026-04-30.2 R -258 -242 TGCTTTTGTGGTGCTTT 7.7 7.1e-05 -9.549 4.147 12 3 ybeF limit START_END D -309 -1 . 0 0 0 0 ybeF site matrix-scan_2026-04-30.3 R -229 -213 AGTGATAAAGAAAATAT 8.8 2.1e-05 -10.754 4.671 1 1 ybeF site matrix-scan_2026-04-30.6 R -144 -128 CGCTTTTGCTCACCATA 8.2 3.2e-05 -10.365 4.502 2 1 ybeF site matrix-scan_2026-04-30.2 D -95 -79 TTTTTTAAATATTATTT 7.6 7.8e-05 -9.454 4.106 3 1 ybjX limit START_END D -165 -1 . 0 0 0 0 ybjX site matrix-scan_2026-04-30.5 D -110 -94 AACAAAACCCTAAAATT 11.4 8.5e-08 -16.275 7.068 1 1 ybjX site matrix-scan_2026-04-30.3 D -117 -101 AAATATCAACAAAACCC 9.1 1.4e-05 -11.150 4.842 2 1 ybjX site matrix-scan_2026-04-30.5 R -78 -62 AACCAAACATCAATAGT 7.5 8.9e-05 -9.331 4.052 3 2 nudJ limit START_END D -60 -1 . 0 0 0 0 nudJ site matrix-scan_2026-04-30.6 D -39 -23 CACGTTACCGTTGCTTG 7.2 1.0e-04 -9.172 3.983 1 1 yncH limit START_END D -126 -1 . 0 0 0 0 yncH site matrix-scan_2026-04-30.3 R -113 -97 AATAAATAACATAATCT 10.7 9.2e-07 -13.904 6.038 1 1 yncH site matrix-scan_2026-04-30.3 R -51 -35 ATTAAAAAACATACCAT 8.4 3.4e-05 -10.282 4.465 2 2 yncH site matrix-scan_2026-04-30.3 R -50 -34 AATTAAAAAACATACCA 7.8 6.7e-05 -9.604 4.171 3 3 yncH site matrix-scan_2026-04-30.2 D -109 -93 TATGTTATTTATTATTC 7.4 9.6e-05 -9.246 4.015 4 1 gadC limit START_END D -206 -1 . 0 0 0 0 gadC site matrix-scan_2026-04-30.2 D -118 -102 TGTTCTGAATACGCTTC 9.2 1.2e-05 -11.363 4.935 1 1 gadB limit START_END D -412 -1 . 0 0 0 0 gadB site matrix-scan_2026-04-30.4 R -249 -233 GTGTTTTATGCTGTTAT 10.2 1.9e-06 -13.190 5.728 1 1 gadB site matrix-scan_2026-04-30.3 R -207 -191 ATTGAAAAACAATACAA 10.1 3.1e-06 -12.697 5.514 2 1 gadB site matrix-scan_2026-04-30.4 R -252 -236 TTTTATGCTGTTATTTT 9.3 9.7e-06 -11.542 5.012 3 2 gadB site matrix-scan_2026-04-30.3 R -147 -131 TTTAAATAACAAAATCC 9.1 1.4e-05 -11.150 4.842 4 2 gadB site matrix-scan_2026-04-30.2 D -290 -274 TTTTTACGTGATAATTC 8.1 4.6e-05 -9.985 4.337 5 1 gadB site matrix-scan_2026-04-30.4 D -393 -377 TCGTTGGCGGGGATTTT 7.7 8.2e-05 -9.411 4.087 6 3 slyB limit START_END D -324 -1 . 0 0 0 0 slyB site matrix-scan_2026-04-30.3 R -197 -181 AATTATAAACAAAACAT 11.1 3.4e-07 -14.899 6.470 1 1 slyB site matrix-scan_2026-04-30.6 D -304 -288 GACGTTTGCGCACCACT 10.2 1.6e-06 -13.330 5.789 2 1 mgrB limit START_END D -209 -1 . 0 0 0 0 ygdR limit START_END D -188 -1 . 0 0 0 0 ygdR site matrix-scan_2026-04-30.4 R -59 -43 TTTTTTCATCCGGTTAT 8.9 1.8e-05 -10.931 4.747 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 -163 -147 AGAAAAACGCTAAACAA 10.5 9.2e-07 -13.896 6.035 1 1 higB site matrix-scan_2026-04-30.6 R -268 -252 CGCGTCTTATCCGGCCT 9.1 9.3e-06 -11.587 5.032 2 1 higB site matrix-scan_2026-04-30.6 R -259 -243 GACGCTTGCCGCGTCTT 8.9 1.2e-05 -11.316 4.915 3 2 higB site matrix-scan_2026-04-30.2 D -153 -137 TTTTTCTACGTTTATTC 8.3 3.6e-05 -10.229 4.442 4 1 higB site matrix-scan_2026-04-30.6 R -315 -299 GGCGTTTACGCCGCATC 8.0 4.1e-05 -10.113 4.392 5 3 higB site matrix-scan_2026-04-30.6 D -279 -263 CACGTTACTCCAGGCCG 7.8 5.2e-05 -9.868 4.286 6 4 higB site matrix-scan_2026-04-30.4 D -163 -147 TTGTTTAGCGTTTTTCT 7.9 6.5e-05 -9.642 4.187 7 1 yrbL limit START_END D -264 -1 . 0 0 0 0 yrbL site matrix-scan_2026-04-30.2 R -148 -132 TTTTCTTAAGGTTCTTC 10.2 2.4e-06 -12.926 5.614 1 1 yrbL site matrix-scan_2026-04-30.5 R -119 -103 AAACAAAACCTAAACAA 9.3 8.4e-06 -11.691 5.077 2 1 yrbL site matrix-scan_2026-04-30.2 D -118 -102 TGTTTAGGTTTTGTTTA 9.3 9.9e-06 -11.525 5.005 3 2 yrbL site matrix-scan_2026-04-30.4 R -214 -198 TTTCAGTACGTGATTTT 7.8 7.3e-05 -9.519 4.134 4 1 zntA limit START_END D -124 -1 . 0 0 0 0 zntA site matrix-scan_2026-04-30.5 D -27 -11 AAGAAAGCCCCTCAATT 9.7 4.5e-06 -12.321 5.351 1 1 zntA site matrix-scan_2026-04-30.4 R -38 -22 TTTCTTGCCGTGATTGT 8.2 4.6e-05 -9.981 4.335 2 1 hdeD limit START_END D -305 -1 . 0 0 0 0 hdeD site matrix-scan_2026-04-30.3 R -83 -67 AATTAAGAAGAAAATCC 9.4 9.3e-06 -11.582 5.030 1 1 hdeD site matrix-scan_2026-04-30.2 R -213 -197 TGATTTTGATATTTTCC 8.3 3.6e-05 -10.229 4.442 2 1 hdeD site matrix-scan_2026-04-30.4 D -119 -103 TTCTTAGACGCGTTTTT 8.2 4.6e-05 -9.981 4.335 3 1 hdeD site matrix-scan_2026-04-30.5 R -119 -103 AAAAACGCGTCTAAGAA 7.4 9.8e-05 -9.231 4.009 4 1 gadE limit START_END D -362 -1 . 0 0 0 0 gadE site matrix-scan_2026-04-30.4 D -279 -263 TTTTTGTTTGCTATTTA 7.9 6.5e-05 -9.642 4.187 1 1 gadA limit START_END D -261 -1 . 0 0 0 0 gadA site matrix-scan_2026-04-30.2 D -204 -188 TGTTTTTAATATTATCA 10.5 1.4e-06 -13.483 5.856 1 1 gadA site matrix-scan_2026-04-30.3 R -147 -131 TTTAAATAACAAAATCC 9.1 1.4e-05 -11.150 4.842 2 1 gadA site matrix-scan_2026-04-30.2 D -153 -137 TGCTTAGGATTTTGTTA 8.5 2.8e-05 -10.471 4.547 3 2 yhjC limit START_END D -570 -1 . 0 0 0 0 yhjC site matrix-scan_2026-04-30.6 R -474 -458 CACGTCATCTCTGTAGA 8.7 1.6e-05 -11.025 4.788 1 1 yhjC site matrix-scan_2026-04-30.6 D -267 -251 CACGTCCTCTGTTCACT 8.6 1.9e-05 -10.888 4.729 2 2 yhjC site matrix-scan_2026-04-30.3 D -112 -96 AACAATAAACAATGCGA 8.5 3.0e-05 -10.398 4.516 3 1 yhjC site matrix-scan_2026-04-30.6 R -177 -161 GGCGATTTCTCAGCAGG 8.1 3.6e-05 -10.239 4.447 4 3 yhjC site matrix-scan_2026-04-30.5 R -384 -368 AGGAAATCCTCAAAATT 8.2 3.9e-05 -10.151 4.408 5 1 yhjC site matrix-scan_2026-04-30.5 D -56 -40 AAGAAATGGATAAAATT 7.8 6.3e-05 -9.667 4.198 6 2 yhjC site matrix-scan_2026-04-30.4 R -309 -293 TCCTTGCCGTTTGTTAT 7.5 1.0e-04 -9.202 3.996 7 1 yiaG limit START_END D -484 -1 . 0 0 0 0 yiaG site matrix-scan_2026-04-30.2 R -165 -149 TGCTCTGGCTATGATTC 10.5 1.4e-06 -13.483 5.856 1 1 yiaG site matrix-scan_2026-04-30.4 R -464 -448 TCGTTGTGCGCTTTTTT 9.6 6.0e-06 -12.022 5.221 2 1 yiaG site matrix-scan_2026-04-30.6 R -420 -404 CAAGCCTGTCCTGGACT 8.0 4.1e-05 -10.113 4.392 3 1 yiaG site matrix-scan_2026-04-30.6 R -445 -429 CACGTCAGACACGCGTG 7.7 5.8e-05 -9.749 4.234 4 2 yidX limit START_END D -328 -1 . 0 0 0 0 yidX site matrix-scan_2026-04-30.6 D -239 -223 CGCGTTTGCCGTGCGTG 11.1 3.0e-07 -15.024 6.525 1 1 yidX site matrix-scan_2026-04-30.2 D -316 -300 TGCTCTGTATGTTCTTC 10.7 9.5e-07 -13.863 6.020 2 1 yidX site matrix-scan_2026-04-30.5 R -41 -25 AAAAAATCCCTTAAAAT 9.0 1.3e-05 -11.226 4.875 3 1 yidX site matrix-scan_2026-04-30.4 R -112 -96 TTCTTTCCCTCCTGTTT 8.5 3.1e-05 -10.375 4.506 4 1 yidX site matrix-scan_2026-04-30.3 D -169 -153 AATGCATAAAAAAATGA 8.3 3.9e-05 -10.163 4.414 5 1 yjbJ limit START_END D -166 -1 . 0 0 0 0 yjbJ site matrix-scan_2026-04-30.2 R -102 -86 TACGTTCACTTTTCTTC 7.5 8.8e-05 -9.339 4.056 1 1 yjeT limit START_END D -132 -1 . 0 0 0 0 yjeT site matrix-scan_2026-04-30.3 R -79 -63 ATAGAAAAAGAAAACCA 10.7 9.2e-07 -13.904 6.038 1 1 yjeT site matrix-scan_2026-04-30.6 D -31 -15 GGCGCTTGCCCTGGTTT 9.8 3.2e-06 -12.658 5.497 2 1 yjeT site matrix-scan_2026-04-30.5 R -86 -70 AAGAAAACCACCGACAT 8.6 2.4e-05 -10.655 4.627 3 1 mgtA limit START_END D -191 -1 . 0 0 0 0 mgtA site matrix-scan_2026-04-30.6 D -142 -126 CGTCCCTGCTCAGCTTT 8.7 1.6e-05 -11.025 4.788 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 -45.900 13.100 59.000 a:0.303 c:0.197 g:0.199 t:0.301 ; 2 matrix-scan_2026-04-30.3 17 4 1 -49.600 13.400 63.000 a:0.303 c:0.197 g:0.199 t:0.301 ; 3 matrix-scan_2026-04-30.4 17 4 1 -42.600 13.000 55.600 a:0.303 c:0.197 g:0.199 t:0.301 ; 4 matrix-scan_2026-04-30.5 17 4 1 -44.900 13.300 58.200 a:0.303 c:0.197 g:0.199 t:0.301 ; 5 matrix-scan_2026-04-30.6 17 4 1 -35.300 14.100 49.400 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 17 12254 ; 3 matrix-scan_2026-04-30.4 17 12254 ; 4 matrix-scan_2026-04-30.5 13 12254 ; 5 matrix-scan_2026-04-30.6 17 12254 ; TOTAL 84 61270 ; Host name rsat ; Job started 2026-04-30.193922 ; Job done 2026-04-30.193933 ; Seconds 10.29 ; user 10.29 ; system 0.02 ; cuser 0.09 ; csystem 0.03