; matrix-scan -v 1 -matrix_format tab -m $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.193656_x0mFKR.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_2026-04-30.193429_hg3tMC.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_2026-04-30.193429_hg3tMC.fasta.fasta.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/04/30/matrix-scan_2026-04-30.193656_x0mFKR.matrix ; Sequence format fasta ; Pseudo counts 1 ; Background model ; Method input ; Markov order 1 ; Strand undef ; Background pseudo-frequency 0.01 ; Residue probabilities ; a 0.32963 ; c 0.19135 ; g 0.17131 ; t 0.30771 ; 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_2026-04-30.3 R -290 -274 CATGCCTTTAGAGGCAT 17.1 4.3e-11 -23.862 10.363 1 1 ompT site matrix-scan_2026-04-30.4 R -291 -275 ATGCCTTTAGAGGCATA 16.7 1.4e-10 -22.715 9.865 2 1 ompT site matrix-scan_2026-04-30.4 D -290 -274 ATGCCTCTAAAGGCATG 16.4 3.9e-10 -21.664 9.409 3 2 ompT site matrix-scan_2026-04-30.2 R -399 -383 GGCTTGCAAGGCTTTAC 15.4 1.1e-09 -20.596 8.945 4 1 ompT site matrix-scan_2026-04-30.2 D -394 -378 GCCTTGCAAGCCATTGC 15.4 1.1e-09 -20.596 8.945 5 2 ompT site matrix-scan_2026-04-30.3 D -291 -275 TATGCCTCTAAAGGCAT 15.1 1.0e-08 -18.415 7.998 6 2 ompT site matrix-scan_2026-04-30.5 R -390 -374 CCTCGCAATGGCTTGCA 14.8 1.5e-08 -17.991 7.813 7 1 ompT site matrix-scan_2026-04-30.5 R -400 -384 GCTTGCAAGGCTTTACA 14.3 3.2e-08 -17.250 7.492 8 2 ompT site matrix-scan_2026-04-30.5 D -403 -387 ACATGTAAAGCCTTGCA 14.1 4.4e-08 -16.937 7.355 9 3 ompT site matrix-scan_2026-04-30.2 R -389 -373 GCCTCGCAATGGCTTGC 13.5 5.6e-08 -16.706 7.255 10 3 ompT site matrix-scan_2026-04-30.5 D -393 -377 CCTTGCAAGCCATTGCG 13.9 5.7e-08 -16.676 7.242 11 4 ompT site matrix-scan_2026-04-30.3 R -396 -380 AATGGCTTGCAAGGCTT 13.4 1.1e-07 -16.025 6.960 12 3 ompT site matrix-scan_2026-04-30.6 R -187 -171 ATGCGCTATCTGTTTTT 12.0 3.8e-07 -14.775 6.417 13 1 ompT site matrix-scan_2026-04-30.3 D -397 -381 AAAGCCTTGCAAGCCAT 10.3 3.9e-06 -12.460 5.411 14 4 ompT site matrix-scan_2026-04-30.3 R -405 -389 CAAGGCTTTACATGTTT 8.4 2.4e-05 -10.656 4.628 15 5 ompT site matrix-scan_2026-04-30.5 R -380 -364 ACACATAAGGCCTCGCA 8.2 2.8e-05 -10.473 4.548 16 5 ompT site matrix-scan_2026-04-30.5 D -287 -271 CCTCTAAAGGCATGGCA 6.8 9.0e-05 -9.312 4.044 17 6 gadB limit START_END D -412 -1 . 0 0 0 0 gadB site matrix-scan_2026-04-30.6 R -44 -28 ATCCGTTACTTGCTTCT 14.9 1.2e-09 -20.525 8.914 1 1 gadB site matrix-scan_2026-04-30.6 R -247 -231 AGGTGTTTTATGCTGTT 10.7 2.2e-06 -13.021 5.655 2 2 gadB site matrix-scan_2026-04-30.4 D -340 -324 ATGCGTTCAAAATAATA 9.2 1.2e-05 -11.349 4.929 3 1 gadB site matrix-scan_2026-04-30.2 D -79 -63 GCGATCCAATCATTTTA 8.8 1.9e-05 -10.893 4.731 4 1 gadB site matrix-scan_2026-04-30.6 R -270 -254 ATGCGCATTCTGTGTCT 7.8 5.1e-05 -9.881 4.291 5 3 mgrB limit START_END D -209 -1 . 0 0 0 0 mgrB site matrix-scan_2026-04-30.6 R -74 -58 CTCCGTTTCACCTACCT 10.3 3.6e-06 -12.548 5.449 1 1 yrbL limit START_END D -264 -1 . 0 0 0 0 yrbL site matrix-scan_2026-04-30.3 D -135 -119 AAAACCTTAAGAGGCAT 13.3 1.2e-07 -15.901 6.906 1 1 yrbL site matrix-scan_2026-04-30.4 R -135 -119 ATGCCTCTTAAGGTTTT 12.6 2.5e-07 -15.193 6.598 2 1 yrbL site matrix-scan_2026-04-30.4 D -134 -118 AAACCTTAAGAGGCATT 12.3 3.7e-07 -14.809 6.432 3 2 yrbL site matrix-scan_2026-04-30.3 R -134 -118 AATGCCTCTTAAGGTTT 8.9 1.5e-05 -11.106 4.823 4 2 gadA limit START_END D -261 -1 . 0 0 0 0 gadA site matrix-scan_2026-04-30.5 D -126 -110 GCCTGTAATGCCTTGCT 15.5 4.7e-09 -19.176 8.328 1 1 gadA site matrix-scan_2026-04-30.6 R -44 -28 ATCCGTTAACAGCTTCT 13.8 1.8e-08 -17.828 7.743 2 1 gadA site matrix-scan_2026-04-30.3 R -128 -112 CAAGGCATTACAGGCTT 13.9 5.8e-08 -16.666 7.238 3 1 gadA site matrix-scan_2026-04-30.2 R -122 -106 TGGAAGCAAGGCATTAC 12.4 2.9e-07 -15.061 6.541 4 1 gadA site matrix-scan_2026-04-30.5 R -123 -107 GGAAGCAAGGCATTACA 7.7 4.3e-05 -10.045 4.362 5 2 ; ; Matrices ; matrix name ncol nrow pseudo Wmin Wmax Wrange ; 1 matrix-scan_2026-04-30.2 17 4 1 -30.500 17.200 47.700 a:0.330 c:0.191 g:0.171 t:0.308 ; 2 matrix-scan_2026-04-30.3 17 4 1 -30.500 17.300 47.800 a:0.330 c:0.191 g:0.171 t:0.308 ; 3 matrix-scan_2026-04-30.4 17 4 1 -30.500 16.800 47.300 a:0.330 c:0.191 g:0.171 t:0.308 ; 4 matrix-scan_2026-04-30.5 17 4 1 -30.500 18.400 48.900 a:0.330 c:0.191 g:0.171 t:0.308 ; 5 matrix-scan_2026-04-30.6 17 4 1 -30.500 15.800 46.300 a:0.330 c:0.191 g:0.171 t:0.308 ; Number of sequences scanned 5 ; Sum of sequence lengths 1620 ; N residues 0 ; Matches per matrix ; matrix name matches scored ; 1 matrix-scan_2026-04-30.2 5 3080 ; 2 matrix-scan_2026-04-30.3 8 3080 ; 3 matrix-scan_2026-04-30.4 5 3080 ; 4 matrix-scan_2026-04-30.5 8 3080 ; 5 matrix-scan_2026-04-30.6 6 3080 ; TOTAL 32 15400 ; Host name rsat ; Job started 2026-04-30.193656 ; Job done 2026-04-30.193701 ; Seconds 4.85 ; user 4.85 ; system 0.03 ; cuser 0.12 ; csystem 0.01