; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/06/02/matrix-scan_2026-06-02.101040_eCrsG9.matrix -pseudo 1 -decimals 1 -2str -origin end -bginput -markov 1 -bg_pseudo 0.01 -return limits -return pval -uth pval 0.0002 -i $RSAT/public_html/tmp/www-data/2026/06/02/tmp_sequence_2026-06-02.101040_56ex1D.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/06/02/tmp_sequence_2026-06-02.101040_56ex1D.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/06/02/matrix-scan_2026-06-02.101040_eCrsG9.matrix ; Sequence format fasta ; Pseudo counts 1 ; Background model ; Method input ; Markov order 1 ; Strand undef ; Background pseudo-frequency 0.01 ; Residue probabilities ; a 0.28891 ; c 0.21973 ; g 0.20122 ; t 0.29014 ; Thresholds lower upper ; pval NA 0.0002 ; 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 PAS_chr1-1_0097 limit START_END D -800 -1 . 0 0 0 0 PAS_chr1-1_0118 limit START_END D -800 -1 . 0 0 0 0 PAS_chr1-1_0226 limit START_END D -800 -1 . 0 0 0 0 PAS_chr1-3_0119 limit START_END D -800 -1 . 0 0 0 0 PAS_chr1-3_0312 limit START_END D -800 -1 . 0 0 0 0 PAS_chr1-4_0327 limit START_END D -800 -1 . 0 0 0 0 PAS_chr1-4_0329 limit START_END D -800 -1 . 0 0 0 0 PAS_chr1-4_0338 limit START_END D -800 -1 . 0 0 0 0 PAS_chr1-4_0392 limit START_END D -800 -1 . 0 0 0 0 PAS_chr1-4_0393 limit START_END D -800 -1 . 0 0 0 0 PAS_chr1-4_0431 limit START_END D -800 -1 . 0 0 0 0 PAS_chr1-4_0668 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-1_0037 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-1_0189 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-1_0242 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-1_0313 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-1_0472 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-1_0640 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-1_0767 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-1_0853 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-2_0022 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-2_0127 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-2_0131 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-2_0208 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-2_0236 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-2_0288 limit START_END D -800 -1 . 0 0 0 0 PAS_chr3_0078 limit START_END D -800 -1 . 0 0 0 0 PAS_chr3_0095 limit START_END D -800 -1 . 0 0 0 0 PAS_chr3_0188 limit START_END D -800 -1 . 0 0 0 0 PAS_chr3_0349 limit START_END D -800 -1 . 0 0 0 0 PAS_chr3_0445 limit START_END D -800 -1 . 0 0 0 0 PAS_chr3_0648 limit START_END D -800 -1 . 0 0 0 0 PAS_chr3_0744 limit START_END D -800 -1 . 0 0 0 0 PAS_chr3_0841 limit START_END D -800 -1 . 0 0 0 0 PAS_chr3_0932 limit START_END D -800 -1 . 0 0 0 0 PAS_chr3_0987 limit START_END D -800 -1 . 0 0 0 0 PAS_chr3_1068 limit START_END D -800 -1 . 0 0 0 0 PAS_chr3_1214 limit START_END D -800 -1 . 0 0 0 0 PAS_chr3_1230 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0042 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0146 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0147 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0151 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0191 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0248 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0314 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0336 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0407 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0470 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0488 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0593 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0627 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0704 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0762 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0809 limit START_END D -800 -1 . 0 0 0 0 PAS_FragB_0015 limit START_END D -800 -1 . 0 0 0 0 PAS_chr1-1_0118 site PHO4 D -527 -520 GCATGTGG 7.1 1.6e-04 -8.740 3.796 PAS_chr1-1_0118 site PHO4 R -527 -520 CCACATGC 6.9 1.9e-04 -8.568 3.721 PAS_chr1-4_0327 site PHO4 D -557 -550 GCATGTGG 7.1 1.6e-04 -8.740 3.796 PAS_chr1-4_0327 site PHO4 R -557 -550 CCACATGC 6.9 1.9e-04 -8.568 3.721 PAS_chr1-4_0392 site PHO4 D -397 -390 GCACATGC 7.4 1.1e-04 -9.115 3.959 PAS_chr1-4_0392 site PHO4 R -397 -390 GCATGTGC 7.4 1.1e-04 -9.115 3.959 PAS_chr1-4_0668 site PHO4 D -278 -271 GCACATGC 7.4 1.1e-04 -9.115 3.959 PAS_chr1-4_0668 site PHO4 R -278 -271 GCATGTGC 7.4 1.1e-04 -9.115 3.959 PAS_chr1-4_0668 site PHO4 D -168 -161 CCACATGC 6.9 1.9e-04 -8.568 3.721 PAS_chr1-4_0668 site PHO4 R -168 -161 GCATGTGG 7.1 1.6e-04 -8.740 3.796 PAS_chr2-2_0288 site PHO4 D -531 -524 CCACATGC 6.9 1.9e-04 -8.568 3.721 PAS_chr2-2_0288 site PHO4 R -531 -524 GCATGTGG 7.1 1.6e-04 -8.740 3.796 PAS_chr3_0078 site PHO4 D -362 -355 GAACGTGC 7.8 6.1e-05 -9.705 4.215 PAS_chr3_0078 site PHO4 R -362 -355 GCACGTTC 7.8 6.1e-05 -9.705 4.215 PAS_chr4_0151 site PHO4 D -560 -553 GAACGTGG 7.5 8.7e-05 -9.350 4.060 PAS_chr4_0151 site PHO4 R -560 -553 CCACGTTC 7.3 1.3e-04 -8.948 3.886 PAS_chr2-1_0853 site RIM101 D -165 -159 CGCCAAG 9.4 3.3e-05 -10.319 4.481 PAS_chr3_0095 site RIM101 D -721 -715 GGCCAAG 7.6 1.4e-04 -8.874 3.854 PAS_chr3_0188 site RIM101 D -332 -326 GGCCAAG 7.6 1.4e-04 -8.874 3.854 PAS_chr3_1230 site RIM101 D -732 -726 GGCCAAG 7.6 1.4e-04 -8.874 3.854 PAS_chr4_0191 site RIM101 D -659 -653 GGCCAAG 7.6 1.4e-04 -8.874 3.854 PAS_chr4_0191 site RIM101 R -53 -47 GGCCAAG 7.6 1.4e-04 -8.874 3.854 PAS_chr4_0762 site RIM101 R -277 -271 GGCCAAG 7.6 1.4e-04 -8.874 3.854 PAS_chr1-4_0327 site MIG1 D -672 -667 CCCCGG 7.2 2.0e-04 -8.517 3.699 PAS_chr1-4_0327 site MIG1 D -53 -48 CCCCGC 7.9 9.7e-05 -9.241 4.013 PAS_chr1-4_0329 site MIG1 R -189 -184 CCCCGC 7.9 9.7e-05 -9.241 4.013 PAS_chr1-4_0338 site MIG1 D -219 -214 CCCCGG 7.2 2.0e-04 -8.517 3.699 PAS_chr1-4_0393 site MIG1 R -460 -455 CCCCGG 7.2 2.0e-04 -8.517 3.699 PAS_chr2-1_0242 site MIG1 R -534 -529 CCCCGG 7.2 2.0e-04 -8.517 3.699 PAS_chr2-1_0313 site MIG1 D -89 -84 CCCCGC 7.9 9.7e-05 -9.241 4.013 PAS_chr2-1_0472 site MIG1 D -261 -256 CCCCGC 7.9 9.7e-05 -9.241 4.013 PAS_chr2-1_0472 site MIG1 R -229 -224 CCCCGG 7.2 2.0e-04 -8.517 3.699 PAS_chr2-1_0853 site MIG1 D -454 -449 CCCCGC 7.9 9.7e-05 -9.241 4.013 PAS_chr2-1_0853 site MIG1 D -168 -163 CCCCGC 7.9 9.7e-05 -9.241 4.013 PAS_chr2-2_0127 site MIG1 D -144 -139 CCCCGC 7.9 9.7e-05 -9.241 4.013 PAS_chr2-2_0131 site MIG1 R -117 -112 CCCCGC 7.9 9.7e-05 -9.241 4.013 PAS_chr2-2_0236 site MIG1 R -629 -624 CCCCGG 7.2 2.0e-04 -8.517 3.699 PAS_chr2-2_0236 site MIG1 D -145 -140 CCCCGC 7.9 9.7e-05 -9.241 4.013 PAS_chr3_0744 site MIG1 R -686 -681 CCCCGG 7.2 2.0e-04 -8.517 3.699 PAS_chr3_0987 site MIG1 R -677 -672 CCCCGG 7.2 2.0e-04 -8.517 3.699 PAS_chr3_1214 site MIG1 R -428 -423 CCCCGC 7.9 9.7e-05 -9.241 4.013 PAS_chr3_1214 site MIG1 D -29 -24 CCCCGG 7.2 2.0e-04 -8.517 3.699 PAS_chr4_0146 site MIG1 D -762 -757 CCCCGG 7.2 2.0e-04 -8.517 3.699 PAS_chr4_0147 site MIG1 D -245 -240 CCCCGG 7.2 2.0e-04 -8.517 3.699 PAS_chr4_0191 site MIG1 D -383 -378 CCCCGG 7.2 2.0e-04 -8.517 3.699 PAS_chr4_0191 site MIG1 R -381 -376 CCCCGG 7.2 2.0e-04 -8.517 3.699 PAS_chr4_0191 site MIG1 D -180 -175 CCCCGG 7.2 2.0e-04 -8.517 3.699 PAS_chr4_0336 site MIG1 D -252 -247 CCCCGG 7.2 2.0e-04 -8.517 3.699 PAS_chr4_0407 site MIG1 D -365 -360 CCCCGC 7.9 9.7e-05 -9.241 4.013 PAS_FragB_0015 site MIG1 R -390 -385 CCCCGC 7.9 9.7e-05 -9.241 4.013 PAS_chr1-4_0327 site MIG2 D -53 -48 CCCCGC 8.2 9.7e-05 -9.241 4.013 PAS_chr1-4_0329 site MIG2 R -189 -184 CCCCGC 8.2 9.7e-05 -9.241 4.013 PAS_chr2-1_0313 site MIG2 D -89 -84 CCCCGC 8.2 9.7e-05 -9.241 4.013 PAS_chr2-1_0472 site MIG2 D -261 -256 CCCCGC 8.2 9.7e-05 -9.241 4.013 PAS_chr2-1_0853 site MIG2 D -454 -449 CCCCGC 8.2 9.7e-05 -9.241 4.013 PAS_chr2-1_0853 site MIG2 D -168 -163 CCCCGC 8.2 9.7e-05 -9.241 4.013 PAS_chr2-2_0127 site MIG2 D -144 -139 CCCCGC 8.2 9.7e-05 -9.241 4.013 PAS_chr2-2_0131 site MIG2 R -117 -112 CCCCGC 8.2 9.7e-05 -9.241 4.013 PAS_chr2-2_0236 site MIG2 D -145 -140 CCCCGC 8.2 9.7e-05 -9.241 4.013 PAS_chr3_1214 site MIG2 R -428 -423 CCCCGC 8.2 9.7e-05 -9.241 4.013 PAS_chr4_0407 site MIG2 D -365 -360 CCCCGC 8.2 9.7e-05 -9.241 4.013 PAS_FragB_0015 site MIG2 R -390 -385 CCCCGC 8.2 9.7e-05 -9.241 4.013 PAS_chr1-1_0097 site NRG1 D -702 -695 TAGGGTCC 8.1 6.0e-05 -9.721 4.222 PAS_chr1-1_0118 site NRG1 R -410 -403 CAGGGTCG 7.3 1.2e-04 -9.028 3.921 PAS_chr1-4_0431 site NRG1 R -446 -439 CAGGGTCT 7.0 1.8e-04 -8.623 3.745 PAS_chr2-1_0189 site NRG1 R -783 -776 AAGGGTCT 7.1 1.7e-04 -8.680 3.770 PAS_chr2-1_0242 site NRG1 R -618 -611 CAGGGTCC 9.7 2.5e-05 -10.597 4.602 PAS_chr2-1_0472 site NRG1 D -589 -582 AAGGGGCC 6.8 1.9e-04 -8.568 3.721 PAS_chr2-1_0767 site NRG1 D -558 -551 CAGGGTCT 7.0 1.8e-04 -8.623 3.745 PAS_chr3_0078 site NRG1 R -180 -173 AAGGGCCC 8.0 7.1e-05 -9.553 4.149 PAS_chr3_0648 site NRG1 R -400 -393 AAGGGTCT 7.1 1.7e-04 -8.680 3.770 PAS_chr3_0841 site NRG1 R -335 -328 AAGGGTTC 7.3 1.2e-04 -9.028 3.921 PAS_chr3_0932 site NRG1 D -373 -366 AAGGGACC 8.3 3.9e-05 -10.152 4.409 PAS_chr3_1068 site NRG1 D -481 -474 AAGGGTCT 7.1 1.7e-04 -8.680 3.770 PAS_chr3_1068 site NRG1 D -245 -238 AAGGGTCG 7.4 9.4e-05 -9.272 4.027 PAS_chr3_1230 site NRG1 D -529 -522 AAGGGTCT 7.1 1.7e-04 -8.680 3.770 PAS_chr4_0151 site NRG1 D -650 -643 CAGGGTCC 9.7 2.5e-05 -10.597 4.602 PAS_chr4_0151 site NRG1 D -617 -610 CAGGGACC 8.1 6.0e-05 -9.721 4.222 PAS_chr4_0248 site NRG1 D -494 -487 AAGGGTCT 7.1 1.7e-04 -8.680 3.770 PAS_chr1-3_0119 site AFT1 R -147 -138 TATCACACCC 7.1 1.1e-04 -9.115 3.959 PAS_chr1-4_0327 site AFT1 R -185 -176 GATTGCACCC 10.2 5.2e-06 -12.167 5.284 PAS_chr1-4_0338 site AFT1 D -235 -226 CCGTGCACCC 6.6 1.6e-04 -8.740 3.796 PAS_chr2-1_0037 site AFT1 D -193 -184 TAATGCACCT 9.0 1.9e-05 -10.871 4.721 PAS_chr2-1_0242 site AFT1 D -319 -310 TTTGGCACCC 7.3 8.8e-05 -9.338 4.056 PAS_chr2-1_0472 site AFT1 D -669 -660 CCTTGCACCC 6.4 1.8e-04 -8.623 3.745 PAS_chr2-1_0472 site AFT1 R -226 -217 ATTCGCACCC 6.4 1.8e-04 -8.623 3.745 PAS_chr2-1_0472 site AFT1 D -156 -147 TAGCGCACCC 9.3 1.5e-05 -11.107 4.824 PAS_chr2-1_0853 site AFT1 R -201 -192 TACTACACCC 7.6 7.0e-05 -9.567 4.155 PAS_chr2-2_0022 site AFT1 R -542 -533 TTGTACACCT 7.0 1.2e-04 -9.028 3.921 PAS_chr2-2_0022 site AFT1 D -263 -254 GATTGCACCA 6.4 1.9e-04 -8.568 3.721 PAS_chr2-2_0131 site AFT1 D -228 -219 CTATGCACCC 7.5 7.5e-05 -9.498 4.125 PAS_chr2-2_0208 site AFT1 R -311 -302 TGTTACACCC 7.0 1.2e-04 -9.028 3.921 PAS_chr3_0078 site AFT1 D -300 -291 CATGGCACCC 6.8 1.4e-04 -8.874 3.854 PAS_chr4_0042 site AFT1 D -221 -212 AAGTACACCC 8.0 5.3e-05 -9.845 4.276 PAS_chr4_0147 site AFT1 D -754 -745 TATTGGACCC 7.1 1.1e-04 -9.115 3.959 PAS_chr4_0248 site AFT1 D -64 -55 GAACGCACCC 6.7 1.5e-04 -8.805 3.824 PAS_chr4_0593 site AFT1 D -551 -542 CTTTGCACCT 6.9 1.3e-04 -8.948 3.886 PAS_chr4_0627 site AFT1 R -408 -399 TATTACACCC 10.1 8.3e-06 -11.699 5.081 ; ; Matrices ; matrix name ncol nrow pseudo Wmin Wmax Wrange ; 1 PHO4 8 4 0 -46.400 10.100 56.500 a:0.289 c:0.220 g:0.201 t:0.290 ; 2 RIM101 7 4 0 -28.900 9.400 38.300 a:0.289 c:0.220 g:0.201 t:0.290 ; 3 MIG1 6 4 0 -21.800 7.900 29.700 a:0.289 c:0.220 g:0.201 t:0.290 ; 4 MIG2 6 4 0 -21.900 8.200 30.100 a:0.289 c:0.220 g:0.201 t:0.290 ; 5 NRG1 8 4 0 -27.600 10.300 37.900 a:0.289 c:0.220 g:0.201 t:0.290 ; 6 CRZ1 6 4 0 -19.400 7.000 26.400 a:0.289 c:0.220 g:0.201 t:0.290 ; 7 AFT1 10 4 0 -27.700 11.700 39.400 a:0.289 c:0.220 g:0.201 t:0.290 ; Number of sequences scanned 56 ; Sum of sequence lengths 44800 ; N residues 0 ; Matches per matrix ; matrix name matches scored ; 1 PHO4 16 0 ; 2 RIM101 7 0 ; 3 MIG1 27 0 ; 4 MIG2 12 0 ; 5 NRG1 17 0 ; 6 CRZ1 0 0 ; 7 AFT1 19 0 ; TOTAL 98 0 ; Host name rsat ; Job started 2026-06-02.101041 ; Job done 2026-06-02.101043 ; Seconds 0.72 ; user 0.72 ; system 0.04 ; cuser 1.4 ; csystem 0.16