; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/06/02/matrix-scan_2026-06-02.103358_c2jazf.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_2026-06-02.103358_zj7PGO.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; 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 ; input $RSAT/public_html/tmp/www-data/2026/06/02/tmp_sequence_2026-06-02.103358_zj7PGO.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/06/02/matrix-scan_2026-06-02.103358_c2jazf.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_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_0097 site CRZ1 D -417 -412 CGCCAC 7.2 8.7e-05 -9.350 4.060 PAS_chr1-1_0226 site CRZ1 D -124 -119 CGCCAC 7.2 8.7e-05 -9.350 4.060 PAS_chr1-4_0668 site CRZ1 D -174 -169 CGCCAC 7.2 8.7e-05 -9.350 4.060 PAS_chr2-1_0242 site CRZ1 R -87 -82 CGCCAC 7.2 8.7e-05 -9.350 4.060 PAS_chr2-2_0288 site CRZ1 R -223 -218 CGCCAC 7.2 8.7e-05 -9.350 4.060 PAS_chr3_1068 site CRZ1 R -574 -569 CGCCAC 7.2 8.7e-05 -9.350 4.060 PAS_chr4_0151 site CRZ1 D -687 -682 CGCCAC 7.2 8.7e-05 -9.350 4.060 ; ; Matrices ; matrix name ncol nrow pseudo Wmin Wmax Wrange ; 1 CRZ1 6 4 0 -19.400 7.200 26.600 a:0.293 c:0.212 g:0.193 t:0.303 ; Number of sequences scanned 56 ; Sum of sequence lengths 44800 ; N residues 0 ; Matches per matrix ; matrix name matches scored ; 1 CRZ1 7 0 ; TOTAL 7 0 ; Host name rsat ; Job started 2026-06-02.103359 ; Job done 2026-06-02.103359 ; Seconds 0.17 ; user 0.17 ; system 0.02 ; cuser 0.28 ; csystem 0.04