; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/06/02/matrix-scan_2026-06-02.110457_Nhaf9H.matrix -pseudo 1 -decimals 1 -2str -origin end -bgfile $RSAT/public_html/data/genomes/Komagataella_pastoris.GCA_000027005.1.62/oligo-frequencies/2nt_upstream-noorf_Komagataella_pastoris.GCA_000027005.1.62-ovlp-1str.freq -bg_pseudo 0.01 -return limits -return pval -uth pval 0.0002 -i $RSAT/public_html/tmp/www-data/2026/06/02/tmp_sequence_2026-06-02.110457_OZSrWC.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/06/02/tmp_sequence_2026-06-02.110457_OZSrWC.fasta ; bg $RSAT/public_html/data/genomes/Komagataella_pastoris.GCA_000027005.1.62/oligo-frequencies/2nt_upstream-noorf_Komagataella_pastoris.GCA_000027005.1.62-ovlp-1str.freq ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/06/02/matrix-scan_2026-06-02.110457_Nhaf9H.matrix ; Sequence format fasta ; Pseudo counts 1 ; Background model ; Method file ; Markov order 1 ; Strand sensitive ; Background pseudo-frequency 0.01 ; Residue probabilities ; a 0.29272 ; c 0.21166 ; g 0.19264 ; t 0.30299 ; 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_c121_0015|PAS_c121_0015 limit START_END D -800 -1 . 0 0 0 0 PAS_chr1-1_0135|PAS_chr1-1_0135 limit START_END D -800 -1 . 0 0 0 0 PAS_chr1-4_0040|PAS_chr1-4_0040 limit START_END D -800 -1 . 0 0 0 0 PAS_chr1-4_0355|PAS_chr1-4_0355 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-1_0103|PAS_chr2-1_0103 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-1_0177|PAS_chr2-1_0177 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-1_0235|PAS_chr2-1_0235 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-1_0579|PAS_chr2-1_0579 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-1_0580|PAS_chr2-1_0580 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-1_0668|PAS_chr2-1_0668 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-1_0685|PAS_chr2-1_0685 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-1_0787|PAS_chr2-1_0787 limit START_END D -800 -1 . 0 0 0 0 PAS_chr2-2_0420|PAS_chr2-2_0420 limit START_END D -800 -1 . 0 0 0 0 PAS_chr3_0505|PAS_chr3_0505 limit START_END D -800 -1 . 0 0 0 0 PAS_chr3_0886|PAS_chr3_0886 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0005|PAS_chr4_0005 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0077|PAS_chr4_0077 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0185|PAS_chr4_0185 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0290|PAS_chr4_0290 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0337|PAS_chr4_0337 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0399|PAS_chr4_0399 limit START_END D -800 -1 . 0 0 0 0 PAS_chr4_0570|PAS_chr4_0570 limit START_END D -800 -1 . 0 0 0 0 PAS_c121_0015|PAS_c121_0015 site PHO4 D -108 -101 CCACGTGT 8.2 4.1e-05 -10.102 4.387 PAS_c121_0015|PAS_c121_0015 site PHO4 R -108 -101 ACACGTGG 8.3 3.5e-05 -10.260 4.456 PAS_chr2-1_0103|PAS_chr2-1_0103 site PHO4 D -323 -316 CCATGTGC 7.2 1.5e-04 -8.805 3.824 PAS_chr2-1_0103|PAS_chr2-1_0103 site PHO4 R -323 -316 GCACATGG 7.3 1.3e-04 -8.948 3.886 PAS_chr2-1_0177|PAS_chr2-1_0177 site PHO4 D -678 -671 GAACGTGG 7.6 9.5e-05 -9.262 4.022 PAS_chr2-1_0177|PAS_chr2-1_0177 site PHO4 R -678 -671 CCACGTTC 7.3 1.3e-04 -8.948 3.886 PAS_chr2-1_0177|PAS_chr2-1_0177 site PHO4 D -241 -234 CCACGTGG 9.9 1.8e-05 -10.925 4.745 PAS_chr2-1_0177|PAS_chr2-1_0177 site PHO4 R -241 -234 CCACGTGG 9.9 1.8e-05 -10.925 4.745 PAS_chr2-1_0235|PAS_chr2-1_0235 site PHO4 D -585 -578 CCACGTTG 7.2 1.5e-04 -8.805 3.824 PAS_chr2-1_0235|PAS_chr2-1_0235 site PHO4 R -585 -578 CAACGTGG 7.3 1.3e-04 -8.948 3.886 PAS_chr2-1_0235|PAS_chr2-1_0235 site PHO4 D -440 -433 CAACGTGG 7.3 1.3e-04 -8.948 3.886 PAS_chr2-1_0235|PAS_chr2-1_0235 site PHO4 R -440 -433 CCACGTTG 7.2 1.5e-04 -8.805 3.824 PAS_chr2-1_0235|PAS_chr2-1_0235 site PHO4 D -415 -408 CCACGTGC 10.2 1.3e-05 -11.251 4.886 PAS_chr2-1_0235|PAS_chr2-1_0235 site PHO4 R -415 -408 GCACGTGG 10.4 7.9e-06 -11.749 5.102 PAS_chr2-1_0235|PAS_chr2-1_0235 site PHO4 D -409 -402 GCGCGTGC 7.8 5.8e-05 -9.755 4.237 PAS_chr2-1_0235|PAS_chr2-1_0235 site PHO4 R -409 -402 GCACGCGC 7.7 6.7e-05 -9.611 4.174 PAS_chr2-1_0668|PAS_chr2-1_0668 site PHO4 D -84 -77 GCACGTGG 10.4 7.9e-06 -11.749 5.102 PAS_chr2-1_0668|PAS_chr2-1_0668 site PHO4 R -84 -77 CCACGTGC 10.2 1.3e-05 -11.251 4.886 PAS_chr2-1_0685|PAS_chr2-1_0685 site PHO4 D -148 -141 GAACGTGC 7.9 4.8e-05 -9.944 4.319 PAS_chr2-1_0685|PAS_chr2-1_0685 site PHO4 R -148 -141 GCACGTTC 7.8 5.8e-05 -9.755 4.237 PAS_chr2-1_0685|PAS_chr2-1_0685 site PHO4 D -126 -119 CCACGTGG 9.9 1.8e-05 -10.925 4.745 PAS_chr2-1_0685|PAS_chr2-1_0685 site PHO4 R -126 -119 CCACGTGG 9.9 1.8e-05 -10.925 4.745 PAS_chr2-2_0420|PAS_chr2-2_0420 site PHO4 D -91 -84 GCACGTGG 10.4 7.9e-06 -11.749 5.102 PAS_chr2-2_0420|PAS_chr2-2_0420 site PHO4 R -91 -84 CCACGTGC 10.2 1.3e-05 -11.251 4.886 PAS_chr4_0077|PAS_chr4_0077 site PHO4 D -355 -348 ACACGTGG 8.3 3.5e-05 -10.260 4.456 PAS_chr4_0077|PAS_chr4_0077 site PHO4 R -355 -348 CCACGTGT 8.2 4.1e-05 -10.102 4.387 PAS_chr4_0077|PAS_chr4_0077 site PHO4 D -247 -240 CCACGTGC 10.2 1.3e-05 -11.251 4.886 PAS_chr4_0077|PAS_chr4_0077 site PHO4 R -247 -240 GCACGTGG 10.4 7.9e-06 -11.749 5.102 PAS_chr4_0077|PAS_chr4_0077 site PHO4 D -238 -231 CAACGTGG 7.3 1.3e-04 -8.948 3.886 PAS_chr4_0077|PAS_chr4_0077 site PHO4 R -238 -231 CCACGTTG 7.2 1.5e-04 -8.805 3.824 PAS_chr4_0077|PAS_chr4_0077 site PHO4 D -150 -143 CCACGTGT 8.2 4.1e-05 -10.102 4.387 PAS_chr4_0077|PAS_chr4_0077 site PHO4 R -150 -143 ACACGTGG 8.3 3.5e-05 -10.260 4.456 PAS_chr4_0290|PAS_chr4_0290 site PHO4 D -85 -78 GCACGTGC 10.6 3.9e-06 -12.455 5.409 PAS_chr4_0290|PAS_chr4_0290 site PHO4 R -85 -78 GCACGTGC 10.6 3.9e-06 -12.455 5.409 PAS_chr4_0337|PAS_chr4_0337 site PHO4 D -373 -366 CCACGTGT 8.2 4.1e-05 -10.102 4.387 PAS_chr4_0337|PAS_chr4_0337 site PHO4 R -373 -366 ACACGTGG 8.3 3.5e-05 -10.260 4.456 PAS_chr4_0337|PAS_chr4_0337 site PHO4 D -98 -91 CCACGTTG 7.2 1.5e-04 -8.805 3.824 PAS_chr4_0337|PAS_chr4_0337 site PHO4 R -98 -91 CAACGTGG 7.3 1.3e-04 -8.948 3.886 PAS_chr4_0570|PAS_chr4_0570 site PHO4 D -109 -102 CCACGTGC 10.2 1.3e-05 -11.251 4.886 PAS_chr4_0570|PAS_chr4_0570 site PHO4 R -109 -102 GCACGTGG 10.4 7.9e-06 -11.749 5.102 PAS_c121_0015|PAS_c121_0015 site RIM101 R -785 -779 CGCCACG 4.2 2.0e-04 -8.517 3.699 PAS_c121_0015|PAS_c121_0015 site RIM101 R -681 -675 AGCCAAG 7.3 1.8e-04 -8.623 3.745 PAS_chr1-4_0355|PAS_chr1-4_0355 site RIM101 D -745 -739 GGCCAAG 7.7 1.3e-04 -8.948 3.886 PAS_chr1-4_0355|PAS_chr1-4_0355 site RIM101 D -615 -609 GGCCAAG 7.7 1.3e-04 -8.948 3.886 PAS_chr2-1_0235|PAS_chr2-1_0235 site RIM101 D -546 -540 GGCCAAG 7.7 1.3e-04 -8.948 3.886 PAS_chr2-1_0235|PAS_chr2-1_0235 site RIM101 R -537 -531 CGCCAAG 9.5 3.1e-05 -10.382 4.509 PAS_chr2-1_0235|PAS_chr2-1_0235 site RIM101 D -417 -411 CGCCACG 4.2 2.0e-04 -8.517 3.699 PAS_chr2-1_0235|PAS_chr2-1_0235 site RIM101 R -165 -159 TGCCAAG 8.8 8.8e-05 -9.338 4.056 PAS_chr2-1_0579|PAS_chr2-1_0579 site RIM101 R -742 -736 AGCCAAG 7.3 1.8e-04 -8.623 3.745 PAS_chr4_0005|PAS_chr4_0005 site RIM101 R -337 -331 TGCCAAG 8.8 8.8e-05 -9.338 4.056 PAS_chr4_0077|PAS_chr4_0077 site RIM101 D -492 -486 AGCCAAG 7.3 1.8e-04 -8.623 3.745 PAS_chr4_0077|PAS_chr4_0077 site RIM101 D -430 -424 TGCCAAG 8.8 8.8e-05 -9.338 4.056 PAS_chr4_0185|PAS_chr4_0185 site RIM101 D -629 -623 GGCCAAG 7.7 1.3e-04 -8.948 3.886 PAS_chr4_0185|PAS_chr4_0185 site RIM101 R -132 -126 CGCCAAG 9.5 3.1e-05 -10.382 4.509 PAS_chr4_0337|PAS_chr4_0337 site RIM101 D -212 -206 AGCCAAG 7.3 1.8e-04 -8.623 3.745 PAS_chr4_0570|PAS_chr4_0570 site RIM101 D -797 -791 GGCCAAG 7.7 1.3e-04 -8.948 3.886 PAS_chr4_0570|PAS_chr4_0570 site RIM101 D -713 -707 GGCCAAG 7.7 1.3e-04 -8.948 3.886 PAS_chr4_0570|PAS_chr4_0570 site RIM101 R -334 -328 AGCCAAG 7.3 1.8e-04 -8.623 3.745 PAS_chr4_0005|PAS_chr4_0005 site MIG1 R -637 -632 CCCCGC 8.2 7.5e-05 -9.498 4.125 PAS_chr4_0570|PAS_chr4_0570 site MIG1 R -678 -673 CCCCGC 8.2 7.5e-05 -9.498 4.125 PAS_chr4_0570|PAS_chr4_0570 site MIG1 R -552 -547 CCCCGC 8.2 7.5e-05 -9.498 4.125 PAS_chr4_0005|PAS_chr4_0005 site MIG2 R -637 -632 CCCCGC 8.5 7.5e-05 -9.498 4.125 PAS_chr4_0570|PAS_chr4_0570 site MIG2 R -678 -673 CCCCGC 8.5 7.5e-05 -9.498 4.125 PAS_chr4_0570|PAS_chr4_0570 site MIG2 R -552 -547 CCCCGC 8.5 7.5e-05 -9.498 4.125 PAS_chr2-1_0235|PAS_chr2-1_0235 site NRG1 R -365 -358 AAGGGTCT 7.2 1.4e-04 -8.874 3.854 PAS_chr4_0077|PAS_chr4_0077 site NRG1 R -297 -290 AAGGGTCT 7.2 1.4e-04 -8.874 3.854 PAS_chr4_0290|PAS_chr4_0290 site NRG1 R -480 -473 CAGGGTCT 7.1 1.6e-04 -8.740 3.796 PAS_chr4_0399|PAS_chr4_0399 site NRG1 R -327 -320 AAGGGTTC 7.3 1.2e-04 -9.028 3.921 PAS_chr4_0570|PAS_chr4_0570 site NRG1 D -575 -568 CAGGGACC 8.4 4.0e-05 -10.127 4.398 PAS_chr4_0570|PAS_chr4_0570 site NRG1 R -459 -452 AAGGGTGC 6.7 1.9e-04 -8.568 3.721 PAS_c121_0015|PAS_c121_0015 site CRZ1 R -784 -779 CGCCAC 7.2 8.7e-05 -9.350 4.060 PAS_chr2-1_0235|PAS_chr2-1_0235 site CRZ1 D -417 -412 CGCCAC 7.2 8.7e-05 -9.350 4.060 PAS_chr2-1_0685|PAS_chr2-1_0685 site CRZ1 D -309 -304 CGCCAC 7.2 8.7e-05 -9.350 4.060 PAS_chr4_0290|PAS_chr4_0290 site CRZ1 R -743 -738 CGCCAC 7.2 8.7e-05 -9.350 4.060 PAS_c121_0015|PAS_c121_0015 site AFT1 D -614 -605 TTTCGCACCC 7.9 6.0e-05 -9.721 4.222 PAS_chr1-1_0135|PAS_chr1-1_0135 site AFT1 D -324 -315 CTATGCACCC 7.8 6.5e-05 -9.641 4.187 PAS_chr2-1_0580|PAS_chr2-1_0580 site AFT1 R -164 -155 TTTTGCACCA 6.1 2.0e-04 -8.517 3.699 PAS_chr4_0077|PAS_chr4_0077 site AFT1 D -643 -634 CTTTACACCC 6.7 1.4e-04 -8.874 3.854 PAS_chr4_0337|PAS_chr4_0337 site AFT1 R -369 -360 GATTGCACAC 6.7 1.4e-04 -8.874 3.854 PAS_chr4_0570|PAS_chr4_0570 site AFT1 D -463 -454 CAGGGCACCC 6.9 1.3e-04 -8.948 3.886 ; ; Matrices ; matrix name ncol nrow pseudo Wmin Wmax Wrange ; 1 PHO4 8 4 0 -46.400 10.300 56.700 a:0.293 c:0.212 g:0.193 t:0.303 ; 2 RIM101 7 4 0 -28.900 9.600 38.500 a:0.293 c:0.212 g:0.193 t:0.303 ; 3 MIG1 6 4 0 -21.900 8.100 30.000 a:0.293 c:0.212 g:0.193 t:0.303 ; 4 MIG2 6 4 0 -21.900 8.500 30.400 a:0.293 c:0.212 g:0.193 t:0.303 ; 5 NRG1 8 4 0 -27.500 10.500 38.000 a:0.293 c:0.212 g:0.193 t:0.303 ; 6 CRZ1 6 4 0 -19.400 7.200 26.600 a:0.293 c:0.212 g:0.193 t:0.303 ; 7 AFT1 10 4 0 -27.500 11.800 39.300 a:0.293 c:0.212 g:0.193 t:0.303 ; Number of sequences scanned 22 ; Sum of sequence lengths 17600 ; N residues 0 ; Matches per matrix ; matrix name matches scored ; 1 PHO4 40 0 ; 2 RIM101 18 0 ; 3 MIG1 3 0 ; 4 MIG2 3 0 ; 5 NRG1 6 0 ; 6 CRZ1 4 0 ; 7 AFT1 6 0 ; TOTAL 80 0 ; Host name rsat ; Job started 2026-06-02.110457 ; Job done 2026-06-02.110500 ; Seconds 0.58 ; user 0.58 ; system 0.05 ; cuser 1.51 ; csystem 0.21