; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/04/19/matrix-scan_2026-04-19.180504_q5IP1j.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 0.0001 -i $RSAT/public_html/tmp/www-data/2026/04/19/tmp_sequence_2026-04-19.180504_v2bDaG.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/04/19/tmp_sequence_2026-04-19.180504_v2bDaG.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/2026/04/19/matrix-scan_2026-04-19.180504_q5IP1j.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 0.0001 ; 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 rand_1 limit START_END D -800 -1 . 0 0 0 0 rand_2 limit START_END D -800 -1 . 0 0 0 0 rand_3 limit START_END D -800 -1 . 0 0 0 0 rand_4 limit START_END D -800 -1 . 0 0 0 0 rand_5 limit START_END D -800 -1 . 0 0 0 0 rand_6 limit START_END D -800 -1 . 0 0 0 0 rand_7 limit START_END D -800 -1 . 0 0 0 0 rand_8 limit START_END D -800 -1 . 0 0 0 0 rand_9 limit START_END D -800 -1 . 0 0 0 0 rand_10 limit START_END D -800 -1 . 0 0 0 0 rand_11 limit START_END D -800 -1 . 0 0 0 0 rand_12 limit START_END D -800 -1 . 0 0 0 0 rand_13 limit START_END D -800 -1 . 0 0 0 0 rand_14 limit START_END D -800 -1 . 0 0 0 0 rand_15 limit START_END D -800 -1 . 0 0 0 0 rand_16 limit START_END D -800 -1 . 0 0 0 0 rand_17 limit START_END D -800 -1 . 0 0 0 0 rand_18 limit START_END D -800 -1 . 0 0 0 0 rand_19 limit START_END D -800 -1 . 0 0 0 0 rand_20 limit START_END D -800 -1 . 0 0 0 0 rand_21 limit START_END D -800 -1 . 0 0 0 0 rand_22 limit START_END D -800 -1 . 0 0 0 0 rand_23 limit START_END D -800 -1 . 0 0 0 0 rand_24 limit START_END D -800 -1 . 0 0 0 0 rand_25 limit START_END D -800 -1 . 0 0 0 0 rand_26 limit START_END D -800 -1 . 0 0 0 0 rand_27 limit START_END D -800 -1 . 0 0 0 0 rand_28 limit START_END D -800 -1 . 0 0 0 0 rand_29 limit START_END D -800 -1 . 0 0 0 0 rand_30 limit START_END D -800 -1 . 0 0 0 0 rand_31 limit START_END D -800 -1 . 0 0 0 0 rand_32 limit START_END D -800 -1 . 0 0 0 0 rand_33 limit START_END D -800 -1 . 0 0 0 0 rand_34 limit START_END D -800 -1 . 0 0 0 0 rand_35 limit START_END D -800 -1 . 0 0 0 0 rand_36 limit START_END D -800 -1 . 0 0 0 0 rand_37 limit START_END D -800 -1 . 0 0 0 0 rand_38 limit START_END D -800 -1 . 0 0 0 0 rand_39 limit START_END D -800 -1 . 0 0 0 0 rand_40 limit START_END D -800 -1 . 0 0 0 0 rand_41 limit START_END D -800 -1 . 0 0 0 0 rand_42 limit START_END D -800 -1 . 0 0 0 0 rand_43 limit START_END D -800 -1 . 0 0 0 0 rand_44 limit START_END D -800 -1 . 0 0 0 0 rand_45 limit START_END D -800 -1 . 0 0 0 0 rand_46 limit START_END D -800 -1 . 0 0 0 0 rand_47 limit START_END D -800 -1 . 0 0 0 0 rand_48 limit START_END D -800 -1 . 0 0 0 0 rand_49 limit START_END D -800 -1 . 0 0 0 0 rand_50 limit START_END D -800 -1 . 0 0 0 0 rand_51 limit START_END D -800 -1 . 0 0 0 0 rand_52 limit START_END D -800 -1 . 0 0 0 0 rand_53 limit START_END D -800 -1 . 0 0 0 0 rand_54 limit START_END D -800 -1 . 0 0 0 0 rand_55 limit START_END D -800 -1 . 0 0 0 0 rand_56 limit START_END D -800 -1 . 0 0 0 0 rand_57 limit START_END D -800 -1 . 0 0 0 0 rand_58 limit START_END D -800 -1 . 0 0 0 0 rand_59 limit START_END D -800 -1 . 0 0 0 0 rand_60 limit START_END D -800 -1 . 0 0 0 0 rand_61 limit START_END D -800 -1 . 0 0 0 0 rand_62 limit START_END D -800 -1 . 0 0 0 0 rand_63 limit START_END D -800 -1 . 0 0 0 0 rand_64 limit START_END D -800 -1 . 0 0 0 0 rand_65 limit START_END D -800 -1 . 0 0 0 0 rand_66 limit START_END D -800 -1 . 0 0 0 0 rand_67 limit START_END D -800 -1 . 0 0 0 0 rand_68 limit START_END D -800 -1 . 0 0 0 0 rand_69 limit START_END D -800 -1 . 0 0 0 0 rand_70 limit START_END D -800 -1 . 0 0 0 0 rand_71 limit START_END D -800 -1 . 0 0 0 0 rand_72 limit START_END D -800 -1 . 0 0 0 0 rand_73 limit START_END D -800 -1 . 0 0 0 0 rand_74 limit START_END D -800 -1 . 0 0 0 0 rand_75 limit START_END D -800 -1 . 0 0 0 0 rand_76 limit START_END D -800 -1 . 0 0 0 0 rand_77 limit START_END D -800 -1 . 0 0 0 0 rand_78 limit START_END D -800 -1 . 0 0 0 0 rand_79 limit START_END D -800 -1 . 0 0 0 0 rand_80 limit START_END D -800 -1 . 0 0 0 0 rand_81 limit START_END D -800 -1 . 0 0 0 0 rand_82 limit START_END D -800 -1 . 0 0 0 0 rand_83 limit START_END D -800 -1 . 0 0 0 0 rand_84 limit START_END D -800 -1 . 0 0 0 0 rand_85 limit START_END D -800 -1 . 0 0 0 0 rand_86 limit START_END D -800 -1 . 0 0 0 0 rand_87 limit START_END D -800 -1 . 0 0 0 0 rand_88 limit START_END D -800 -1 . 0 0 0 0 rand_89 limit START_END D -800 -1 . 0 0 0 0 rand_90 limit START_END D -800 -1 . 0 0 0 0 rand_91 limit START_END D -800 -1 . 0 0 0 0 rand_92 limit START_END D -800 -1 . 0 0 0 0 rand_93 limit START_END D -800 -1 . 0 0 0 0 rand_94 limit START_END D -800 -1 . 0 0 0 0 rand_95 limit START_END D -800 -1 . 0 0 0 0 rand_96 limit START_END D -800 -1 . 0 0 0 0 rand_97 limit START_END D -800 -1 . 0 0 0 0 rand_98 limit START_END D -800 -1 . 0 0 0 0 rand_99 limit START_END D -800 -1 . 0 0 0 0 rand_100 limit START_END D -800 -1 . 0 0 0 0 rand_7 site PHO4 D -467 -460 CCACGTGT 8.2 4.1e-05 -10.102 4.387 rand_7 site PHO4 R -467 -460 ACACGTGG 8.3 3.5e-05 -10.260 4.456 rand_20 site PHO4 D -520 -513 CCACGTGG 9.9 1.8e-05 -10.925 4.745 rand_20 site PHO4 R -520 -513 CCACGTGG 9.9 1.8e-05 -10.925 4.745 rand_23 site PHO4 D -781 -774 ACACGTGG 8.3 3.5e-05 -10.260 4.456 rand_23 site PHO4 R -781 -774 CCACGTGT 8.2 4.1e-05 -10.102 4.387 rand_25 site PHO4 D -282 -275 GAACGTGC 7.9 4.8e-05 -9.944 4.319 rand_25 site PHO4 R -282 -275 GCACGTTC 7.8 5.8e-05 -9.755 4.237 rand_30 site PHO4 D -635 -628 GCATGTGC 7.7 6.7e-05 -9.611 4.174 rand_30 site PHO4 R -635 -628 GCACATGC 7.6 9.5e-05 -9.262 4.022 rand_45 site PHO4 D -60 -53 GCATGTGC 7.7 6.7e-05 -9.611 4.174 rand_45 site PHO4 R -60 -53 GCACATGC 7.6 9.5e-05 -9.262 4.022 rand_52 site PHO4 R -21 -14 GAACGTGG 7.6 9.5e-05 -9.262 4.022 rand_54 site PHO4 D -557 -550 GCACGTTG 7.6 9.5e-05 -9.262 4.022 rand_54 site PHO4 R -557 -550 CAACGTGC 7.6 9.5e-05 -9.262 4.022 rand_64 site PHO4 D -298 -291 CCACGTGC 10.2 1.3e-05 -11.251 4.886 rand_64 site PHO4 R -298 -291 GCACGTGG 10.4 7.9e-06 -11.749 5.102 rand_65 site PHO4 D -594 -587 GCACGTTG 7.6 9.5e-05 -9.262 4.022 rand_65 site PHO4 R -594 -587 CAACGTGC 7.6 9.5e-05 -9.262 4.022 rand_65 site PHO4 D -519 -512 GCATGTGC 7.7 6.7e-05 -9.611 4.174 rand_65 site PHO4 R -519 -512 GCACATGC 7.6 9.5e-05 -9.262 4.022 rand_76 site PHO4 D -86 -79 GCACATGC 7.6 9.5e-05 -9.262 4.022 rand_76 site PHO4 R -86 -79 GCATGTGC 7.7 6.7e-05 -9.611 4.174 rand_95 site PHO4 D -17 -10 GCACGTGG 10.4 7.9e-06 -11.749 5.102 rand_95 site PHO4 R -17 -10 CCACGTGC 10.2 1.3e-05 -11.251 4.886 rand_3 site RIM101 D -287 -281 TGCCAAG 8.8 8.8e-05 -9.338 4.056 rand_8 site RIM101 D -707 -701 TGCCAAG 8.8 8.8e-05 -9.338 4.056 rand_9 site RIM101 R -20 -14 CGCCAAG 9.5 3.1e-05 -10.382 4.509 rand_13 site RIM101 D -74 -68 TGCCAAG 8.8 8.8e-05 -9.338 4.056 rand_17 site RIM101 R -269 -263 CGCCAAG 9.5 3.1e-05 -10.382 4.509 rand_21 site RIM101 D -384 -378 TGCCAAG 8.8 8.8e-05 -9.338 4.056 rand_23 site RIM101 R -603 -597 CGCCAAG 9.5 3.1e-05 -10.382 4.509 rand_29 site RIM101 D -658 -652 TGCCAAG 8.8 8.8e-05 -9.338 4.056 rand_58 site RIM101 D -402 -396 TGCCAAG 8.8 8.8e-05 -9.338 4.056 rand_73 site RIM101 D -754 -748 CGCCAAG 9.5 3.1e-05 -10.382 4.509 rand_81 site RIM101 R -737 -731 TGCCAAG 8.8 8.8e-05 -9.338 4.056 rand_96 site RIM101 R -310 -304 TGCCAAG 8.8 8.8e-05 -9.338 4.056 rand_21 site NRG1 D -45 -38 AAGGGTCG 7.5 8.1e-05 -9.421 4.092 rand_42 site NRG1 R -603 -596 GAGGGTCC 7.4 9.4e-05 -9.272 4.027 rand_45 site NRG1 D -404 -397 AAGGGCCC 8.2 6.3e-05 -9.672 4.201 rand_60 site NRG1 D -123 -116 AAGGGACC 8.5 3.2e-05 -10.350 4.495 rand_61 site NRG1 D -773 -766 AAGGGCCC 8.2 6.3e-05 -9.672 4.201 rand_62 site NRG1 R -344 -337 AAGGGCCC 8.2 6.3e-05 -9.672 4.201 rand_82 site NRG1 R -473 -466 AAGGGACC 8.5 3.2e-05 -10.350 4.495 rand_92 site NRG1 D -363 -356 CAGGGCCC 8.2 6.3e-05 -9.672 4.201 rand_12 site CRZ1 D -498 -493 CGCCAC 7.2 8.7e-05 -9.350 4.060 rand_18 site CRZ1 D -340 -335 CGCCAC 7.2 8.7e-05 -9.350 4.060 rand_42 site CRZ1 D -410 -405 CGCCAC 7.2 8.7e-05 -9.350 4.060 rand_62 site CRZ1 R -735 -730 CGCCAC 7.2 8.7e-05 -9.350 4.060 rand_62 site CRZ1 R -629 -624 CGCCAC 7.2 8.7e-05 -9.350 4.060 rand_63 site CRZ1 R -151 -146 CGCCAC 7.2 8.7e-05 -9.350 4.060 rand_69 site CRZ1 D -410 -405 CGCCAC 7.2 8.7e-05 -9.350 4.060 rand_78 site CRZ1 D -798 -793 CGCCAC 7.2 8.7e-05 -9.350 4.060 rand_86 site CRZ1 D -240 -235 CGCCAC 7.2 8.7e-05 -9.350 4.060 rand_95 site CRZ1 D -573 -568 CGCCAC 7.2 8.7e-05 -9.350 4.060 ; ; 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 NRG1 8 4 0 -27.500 10.500 38.000 a:0.293 c:0.212 g:0.193 t:0.303 ; 4 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 100 ; Sum of sequence lengths 80000 ; N residues 0 ; Matches per matrix ; matrix name matches scored ; 1 PHO4 25 0 ; 2 RIM101 12 0 ; 3 NRG1 8 0 ; 4 CRZ1 10 0 ; TOTAL 55 0 ; Host name rsat ; Job started 2026-04-19.180505 ; Job done 2026-04-19.180506 ; Seconds 0.41 ; user 0.41 ; system 0.06 ; cuser 0.92 ; csystem 0.14