; matrix-scan -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/05/29/matrix-scan_2026-05-29.144023_ZmzffJ.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/2026/05/29/tmp_sequence_2026-05-29.144023_0ABB6n.fasta -seq_format fasta -n score ; Slow counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/05/29/tmp_sequence_2026-05-29.144023_0ABB6n.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/05/29/matrix-scan_2026-05-29.144023_ZmzffJ.matrix ; Sequence format fasta ; Pseudo counts 1 ; Background model ; Method input ; Markov order 1 ; Strand undef ; Background pseudo-frequency 0.01 ; Residue probabilities ; a 0.33779 ; c 0.20939 ; g 0.14334 ; t 0.30948 ; 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 BVRB_3g059400|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_3g059400 limit START_END D -455 -1 . 0 0 0 0 BVRB_3g059400|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_3g059400 site dyads_test_vs_ctrl_m1 R -336 -318 GGTTCATGAATCATGCCTT 10.8 2.5e-06 -12.880 5.594 1 1 BVRB_4g096340|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_4g096340 limit START_END D -701 -1 . 0 0 0 0 T459_03445|Capsicum_annuum.ASM51225v2.60|T459_03445 limit START_END D -701 -1 . 0 0 0 0 T459_03445|Capsicum_annuum.ASM51225v2.60|T459_03445 site dyads_test_vs_ctrl_m1 R -20 -2 CCCGCACATAGTGGGCCGG 6.9 6.8e-05 -9.597 4.168 1 1 T459_31204|Capsicum_annuum.ASM51225v2.60|T459_31204 limit START_END D -701 -1 . 0 0 0 0 T459_31204|Capsicum_annuum.ASM51225v2.60|T459_31204 site dyads_test_vs_ctrl_m1 D -329 -311 GCTGAATGTTTCATGCCAC 10.1 4.9e-06 -12.217 5.306 1 1 AUR62023693.v1.0|Chenopodium_quinoa.PI614886.392.v1.JGI|AUR62023693.v1.0 limit START_END D -701 -1 . 0 0 0 0 AUR62023693.v1.0|Chenopodium_quinoa.PI614886.392.v1.JGI|AUR62023693.v1.0 site dyads_test_vs_ctrl_m1 R -269 -251 GCGGCATGCTTCGAGCCTT 13.6 1.1e-07 -16.034 6.963 1 1 AUR62023693.v1.0|Chenopodium_quinoa.PI614886.392.v1.JGI|AUR62023693.v1.0 site dyads_test_vs_ctrl_m1 D -269 -251 AAGGCTCGAAGCATGCCGC 10.5 3.4e-06 -12.601 5.472 2 2 AUR62023693.v1.0|Chenopodium_quinoa.PI614886.392.v1.JGI|AUR62023693.v1.0 site dyads_test_vs_ctrl_m1 R -305 -287 CGCGGATGATTCATGCCTT 9.8 6.5e-06 -11.943 5.187 3 3 Cla97C08G153070|Citrullus_lanatus.Cla97_v1.62|Cla97C08G153070 limit START_END D -701 -1 . 0 0 0 0 Cla97C08G153070|Citrullus_lanatus.Cla97_v1.62|Cla97C08G153070 site dyads_test_vs_ctrl_m1 D -212 -194 TCGGGTTGATAATGGCCGC 7.4 4.7e-05 -9.969 4.330 1 1 Cla97C08G153070|Citrullus_lanatus.Cla97_v1.62|Cla97C08G153070 site dyads_test_vs_ctrl_m1 R -98 -80 TTTGCAGAAAGTGTGCCCT 6.3 1.0e-04 -9.165 3.980 2 2 MELO3C011439.2|Cucumis_melo.Melonv4.60|MELO3C011439.2 limit START_END D -701 -1 . 0 0 0 0 Csa_6G366300|Cucumis_sativus.ASM407v2.60|Csa_6G366300 limit START_END D -701 -1 . 0 0 0 0 Csa_6G366300|Cucumis_sativus.ASM407v2.60|Csa_6G366300 site dyads_test_vs_ctrl_m1 R -618 -600 GAAGCACGAATCAAGCCAT 11.2 1.7e-06 -13.277 5.766 1 1 HanXRQr2_Chr13g0574171|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr13g0574171 limit START_END D -701 -1 . 0 0 0 0 HanXRQr2_Chr13g0574171|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr13g0574171 site dyads_test_vs_ctrl_m1 R -374 -356 GATGCATGAGAATGGCCTT 13.8 8.3e-08 -16.306 7.082 1 1 HanXRQr2_Chr13g0574171|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr13g0574171 site dyads_test_vs_ctrl_m1 R -273 -255 GATGCATGAGAATGGCCTT 13.8 8.3e-08 -16.306 7.082 2 2 HanXRQr2_Chr13g0574171|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr13g0574171 site dyads_test_vs_ctrl_m1 D -363 -345 CATGCATCCGACAGNNNNN 6.3 1.0e-04 -9.165 3.980 3 3 HanXRQr2_Chr13g0574181|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr13g0574181 limit START_END D -701 -1 . 0 0 0 0 gene-LSAT_8X33320|Lactuca_sativa.Lsat_Salinas_v7.60|gene-LSAT_8X33320 limit START_END D -701 -1 . 0 0 0 0 gene-LSAT_8X33320|Lactuca_sativa.Lsat_Salinas_v7.60|gene-LSAT_8X33320 site dyads_test_vs_ctrl_m1 D -408 -390 TTTGCATGAAACATGCCAA 12.3 5.3e-07 -14.457 6.279 1 1 gene-LSAT_8X33320|Lactuca_sativa.Lsat_Salinas_v7.60|gene-LSAT_8X33320 site dyads_test_vs_ctrl_m1 R -408 -390 TTGGCATGTTTCATGCAAA 7.2 5.5e-05 -9.811 4.261 2 2 gene25542|Medicago_truncatula.MtrunA17r50ANR.60|gene25542 limit START_END D -701 -1 . 0 0 0 0 107761937|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107761937 limit START_END D -701 -1 . 0 0 0 0 107761937|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107761937 site dyads_test_vs_ctrl_m1 D -331 -313 AAGGCATGAGACAGGCCGA 16.7 4.5e-10 -21.516 9.344 1 1 107761937|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107761937 site dyads_test_vs_ctrl_m1 R -331 -313 TCGGCCTGTCTCATGCCTT 12.6 3.8e-07 -14.789 6.423 2 2 107761937|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107761937 site dyads_test_vs_ctrl_m1 R -578 -560 TCGTAATGGATCGGGCCAG 7.1 5.9e-05 -9.744 4.232 3 3 107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142 limit START_END D -701 -1 . 0 0 0 0 107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142 site dyads_test_vs_ctrl_m1 D -171 -153 CCAGCATGGGGCAGGCCGA 15.3 7.8e-09 -18.664 8.105 1 1 107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142 site dyads_test_vs_ctrl_m1 R -146 -128 TTGGCATGTCCTATGCCTT 11.9 8.2e-07 -14.016 6.087 2 2 107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142 site dyads_test_vs_ctrl_m1 D -146 -128 AAGGCATAGGACATGCCAA 11.3 1.5e-06 -13.388 5.814 3 3 107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142 site dyads_test_vs_ctrl_m1 R -121 -103 AGTGCCATATTCACGCCGA 6.4 9.7e-05 -9.236 4.011 4 4 107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142 site dyads_test_vs_ctrl_m1 R -171 -153 TCGGCCTGCCCCATGCTGG 6.3 1.0e-04 -9.165 3.980 5 5 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 limit START_END D -701 -1 . 0 0 0 0 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site dyads_test_vs_ctrl_m1 D -277 -259 CCGGCATGGGACAGGCCGA 17.4 8.1e-11 -23.240 10.093 1 1 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site dyads_test_vs_ctrl_m1 D -252 -234 AAGGCATGGGACATGCCGA 15.8 3.1e-09 -19.583 8.505 2 2 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site dyads_test_vs_ctrl_m1 R -252 -234 TCGGCATGTCCCATGCCTT 14.4 3.4e-08 -17.188 7.464 3 3 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site dyads_test_vs_ctrl_m1 R -277 -259 TCGGCCTGTCCCATGCCGG 11.7 1.0e-06 -13.792 5.990 4 4 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site dyads_test_vs_ctrl_m1 R -227 -209 AGTGCCATATTCACGCCGA 6.4 9.7e-05 -9.236 4.011 5 5 107812499|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107812499 limit START_END D -701 -1 . 0 0 0 0 107812499|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107812499 site dyads_test_vs_ctrl_m1 D -315 -297 AAGGCATGGGACGGGCCGA 16.0 2.1e-09 -19.999 8.686 1 1 107812499|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107812499 site dyads_test_vs_ctrl_m1 R -315 -297 TCGGCCCGTCCCATGCCTT 11.4 1.4e-06 -13.490 5.859 2 2 gene-LOC110794951|Spinacia_oleracea.GCF020520425.1.RefSeq|gene-LOC110794951 limit START_END D -701 -1 . 0 0 0 0 gene-LOC110794951|Spinacia_oleracea.GCF020520425.1.RefSeq|gene-LOC110794951 site dyads_test_vs_ctrl_m1 D -154 -136 ACAGCTCGAAGCACGCCGC 9.9 5.9e-06 -12.043 5.230 1 1 gene-LOC110794951|Spinacia_oleracea.GCF020520425.1.RefSeq|gene-LOC110794951 site dyads_test_vs_ctrl_m1 R -312 -294 GTTGGAAGTCTAAGGCCCT 8.6 1.8e-05 -10.909 4.738 2 2 gene-LOC110794951|Spinacia_oleracea.GCF020520425.1.RefSeq|gene-LOC110794951 site dyads_test_vs_ctrl_m1 R -198 -180 TTGCGATGTTTCATGCCTT 6.6 8.5e-05 -9.379 4.073 3 3 ; ; Matrices ; matrix name ncol nrow pseudo Wmin Wmax Wrange ; 1 dyads_test_vs_ctrl_m1 19 4 1 -33.900 19.600 53.500 a:0.338 c:0.209 g:0.143 t:0.309 ; Number of sequences scanned 17 ; Sum of sequence lengths 11671 ; N residues 2211 ; Matches per matrix ; matrix name matches scored ; 1 dyads_test_vs_ctrl_m1 32 22730 ; TOTAL 32 22730 ; Host name rsat ; Job started 2026-05-29.144023 ; Job done 2026-05-29.144027 ; Seconds 3.35 ; user 3.35 ; system 0.04 ; cuser 0.1 ; csystem 0.02