; matrix-scan -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/06/17/matrix-scan_2026-06-17.043243_s84Sf6.matrix -pseudo 1 -decimals 1 -2str -origin end -offset -200 -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/2026/06/17/tmp_sequence_2026-06-17.043243_qiB7i2.fasta -seq_format fasta -n score ; Slow counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/06/17/tmp_sequence_2026-06-17.043243_qiB7i2.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/06/17/matrix-scan_2026-06-17.043243_s84Sf6.matrix ; Sequence format fasta ; Pseudo counts 1 ; Background model ; Method input ; Markov order 1 ; Strand undef ; Background pseudo-frequency 0.01 ; Residue probabilities ; a 0.34242 ; c 0.18661 ; g 0.15145 ; t 0.31953 ; 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 -255 199 . 0 0 0 0 BVRB_4g096340|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_4g096340 limit START_END D -1501 199 . 0 0 0 0 BVRB_4g096340|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_4g096340 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R 152 164 ATGGGGAAGAAAA 8.4 2.9e-05 -10.456 4.541 1 1 BVRB_4g096340|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_4g096340 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R -184 -172 AGAGGAAAGAGAA 7.5 8.8e-05 -9.340 4.056 2 2 T459_03445|Capsicum_annuum.ASM51225v2.60|T459_03445 limit START_END D -1501 199 . 0 0 0 0 T459_03445|Capsicum_annuum.ASM51225v2.60|T459_03445 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R 26 38 GTGGGACAGAACT 8.1 4.4e-05 -10.036 4.358 1 1 T459_03445|Capsicum_annuum.ASM51225v2.60|T459_03445 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 D -1084 -1072 TTGGGATAGATGT 7.6 7.8e-05 -9.453 4.105 2 2 T459_31204|Capsicum_annuum.ASM51225v2.60|T459_31204 limit START_END D -1501 199 . 0 0 0 0 T459_31204|Capsicum_annuum.ASM51225v2.60|T459_31204 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 D -1018 -1006 GTGAGATAGAGAG 9.6 8.1e-06 -11.724 5.092 1 1 AUR62023693.v1.0|Chenopodium_quinoa.PI614886.392.v1.JGI|AUR62023693.v1.0 limit START_END D -1501 199 . 0 0 0 0 AUR62023693.v1.0|Chenopodium_quinoa.PI614886.392.v1.JGI|AUR62023693.v1.0 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R 1 13 TGGGGTGAGTGCG 7.4 9.6e-05 -9.251 4.018 1 1 Cla97C08G153070|Citrullus_lanatus.Cla97_v1.62|Cla97C08G153070 limit START_END D -1501 199 . 0 0 0 0 Cla97C08G153070|Citrullus_lanatus.Cla97_v1.62|Cla97C08G153070 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 D -432 -420 TCGGTAAAGAGAC 7.7 7.1e-05 -9.550 4.148 1 1 Cla97C08G153070|Citrullus_lanatus.Cla97_v1.62|Cla97C08G153070 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 D -1441 -1429 ATGGGTTAGAAAA 7.5 8.8e-05 -9.340 4.056 2 2 MELO3C011439.2|Cucumis_melo.Melonv4.60|MELO3C011439.2 limit START_END D -1501 199 . 0 0 0 0 MELO3C011439.2|Cucumis_melo.Melonv4.60|MELO3C011439.2 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R -1326 -1314 TTTGGAGAGAGAA 8.1 4.4e-05 -10.036 4.358 1 1 Csa_6G366300|Cucumis_sativus.ASM407v2.60|Csa_6G366300 limit START_END D -1501 199 . 0 0 0 0 HanXRQr2_Chr13g0574171|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr13g0574171 limit START_END D -1501 199 . 0 0 0 0 HanXRQr2_Chr13g0574171|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr13g0574171 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R 182 194 GAGGGATAGAGAA 11.4 3.0e-07 -15.009 6.518 1 1 HanXRQr2_Chr13g0574181|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr13g0574181 limit START_END D -1501 199 . 0 0 0 0 HanXRQr2_Chr13g0574181|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr13g0574181 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R 181 193 AAGGGATAGAGAA 10.9 1.3e-06 -13.568 5.893 1 1 gene-LSAT_8X33320|Lactuca_sativa.Lsat_Salinas_v7.60|gene-LSAT_8X33320 limit START_END D -1501 199 . 0 0 0 0 gene25542|Medicago_truncatula.MtrunA17r50ANR.60|gene25542 limit START_END D -1501 199 . 0 0 0 0 gene25542|Medicago_truncatula.MtrunA17r50ANR.60|gene25542 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R -12 0 TAGGGTGTGAGAG 8.3 3.3e-05 -10.312 4.478 1 1 107761937|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107761937 limit START_END D -1501 199 . 0 0 0 0 107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142 limit START_END D -1501 199 . 0 0 0 0 107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 D -43 -31 AAGGGAAAGAGTA 10.0 5.7e-06 -12.083 5.248 1 1 107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R -677 -665 AGGGTAGAGAGGC 8.0 5.0e-05 -9.910 4.304 2 2 107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R -675 -663 CTAGGGTAGAGAG 7.4 9.6e-05 -9.251 4.018 3 3 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 limit START_END D -1501 199 . 0 0 0 0 107812499|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107812499 limit START_END D -1501 199 . 0 0 0 0 107812499|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107812499 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 D -444 -432 AAGGGATAGAAAG 9.1 1.2e-05 -11.290 4.903 1 1 107812499|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107812499 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 D -818 -806 TAAGGAAAGAGCG 8.1 4.4e-05 -10.036 4.358 2 2 gene-LOC110794951|Spinacia_oleracea.GCF020520425.1.RefSeq|gene-LOC110794951 limit START_END D -1501 199 . 0 0 0 0 gene-LOC110794951|Spinacia_oleracea.GCF020520425.1.RefSeq|gene-LOC110794951 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 D -1153 -1141 NNNNGGAAGAGAG 8.2 3.8e-05 -10.172 4.418 1 1 AT3G13610|Arabidopsis_thaliana.TAIR10.60|F6'H1 limit START_END D -1501 199 . 0 0 0 0 AT3G13610|Arabidopsis_thaliana.TAIR10.60|F6'H1 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 D -430 -418 CTGTGGAAGAGAA 7.5 8.8e-05 -9.340 4.056 1 1 GSBRNA2T00023848001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC05g39690D limit START_END D -1448 199 . 0 0 0 0 GSBRNA2T00023848001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC05g39690D site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R 9 21 GCGGTAGAGAGAG 9.3 1.0e-05 -11.485 4.988 1 1 GSBRNA2T00023848001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC05g39690D site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R -876 -864 TAGGTGGAGAGGC 8.0 5.0e-05 -9.910 4.304 2 2 GSBRNA2T00104708001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA05g25780D limit START_END D -1501 199 . 0 0 0 0 GSBRNA2T00104708001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA05g25780D site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R 9 21 GCGGTAGAGAGAG 9.3 1.0e-05 -11.485 4.988 1 1 GSBRNA2T00104708001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA05g25780D site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R -884 -872 TAGGTGGAGAGGC 8.0 5.0e-05 -9.910 4.304 2 2 GSBRNA2T00123637001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC03g38030D limit START_END D -1501 199 . 0 0 0 0 GSBRNA2T00123637001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC03g38030D site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R 9 21 ACGGTAGAGAGTG 7.7 7.1e-05 -9.550 4.148 1 1 GSBRNA2T00137685001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA03g32900D limit START_END D -1459 199 . 0 0 0 0 GSBRNA2T00137685001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA03g32900D site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 D -1098 -1086 CAGAGAGAGAGAT 9.0 1.4e-05 -11.205 4.866 1 1 GSBRNA2T00137685001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA03g32900D site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R -1068 -1056 GAGGCAGAGAGGG 8.5 2.5e-05 -10.597 4.602 2 2 GSBRNA2T00137685001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA03g32900D site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R -1066 -1054 AAGAGGCAGAGAG 8.5 2.5e-05 -10.597 4.602 3 3 GSBRNA2T00137685001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA03g32900D site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R 9 21 AAGGTAGAGAGTG 8.0 5.0e-05 -9.910 4.304 4 4 A03p040480.1_BraROA|Brassica_rapa_ro18.SCU_BraROA_2.3.60|A03p040480.1_BraROA limit START_END D -1426 199 . 0 0 0 0 A03p040480.1_BraROA|Brassica_rapa_ro18.SCU_BraROA_2.3.60|A03p040480.1_BraROA site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R 9 21 AAGGTAGAGAGTG 8.0 5.0e-05 -9.910 4.304 1 1 GLYMA_07G124400|Glycine_max.Glycine_max_v2.1.60|GLYMA_07G124400 limit START_END D -1501 199 . 0 0 0 0 gene-Lalb_Chr13g0290931|Lupinus_albus.CNRS_Lalb_10.GCA_009771035.1.NCBI|gene-Lalb_Chr13g0290931 limit START_END D -1501 199 . 0 0 0 0 gene-Lalb_Chr13g0290931|Lupinus_albus.CNRS_Lalb_10.GCA_009771035.1.NCBI|gene-Lalb_Chr13g0290931 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 D 178 190 TTGGAAGAGAGAA 7.4 9.6e-05 -9.251 4.018 1 1 107763182|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107763182 limit START_END D -1501 199 . 0 0 0 0 107785648|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107785648 limit START_END D -1501 199 . 0 0 0 0 107785648|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107785648 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R -1431 -1419 CGGGGAAGGAGAG 8.3 3.3e-05 -10.312 4.478 1 1 107796566|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107796566 limit START_END D -1501 199 . 0 0 0 0 107787976|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107787976 limit START_END D -1501 199 . 0 0 0 0 107787976|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107787976 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R -88 -76 TCGGGAAGGAGAG 8.1 4.4e-05 -10.036 4.358 1 1 107787976|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107787976 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R 35 47 AGGGGAAAGTGAG 7.9 5.6e-05 -9.795 4.254 2 2 107787976|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107787976 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 D -694 -682 GTGGGGGAGTGGA 7.5 8.8e-05 -9.340 4.056 3 3 107787976|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107787976 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R 186 198 TTGGGAAAGACCC 7.4 9.6e-05 -9.251 4.018 4 4 Prudul26B000915|Prunus_dulcis.ALMONDv2.60|Prudul26B000915 limit START_END D -773 199 . 0 0 0 0 Prudul26B000915|Prunus_dulcis.ALMONDv2.60|Prudul26B000915 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 D -679 -667 ATGGGGAAGAGAA 10.7 2.1e-06 -13.088 5.684 1 1 Prudul26B000915|Prunus_dulcis.ALMONDv2.60|Prudul26B000915 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 D -700 -688 GAGGGGAAGATAG 9.2 1.1e-05 -11.398 4.950 2 2 Prudul26B000915|Prunus_dulcis.ALMONDv2.60|Prudul26B000915 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R -763 -751 CAGAGTGAGAGAG 8.6 2.2e-05 -10.729 4.659 3 3 Prudul26B000915|Prunus_dulcis.ALMONDv2.60|Prudul26B000915 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R -757 -745 GAGAGACAGAGTG 8.0 5.0e-05 -9.910 4.304 4 4 Prudul26B000915|Prunus_dulcis.ALMONDv2.60|Prudul26B000915 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R -765 -753 GAGTGAGAGAGTT 7.7 7.1e-05 -9.550 4.148 5 5 Prudul26B000915|Prunus_dulcis.ALMONDv2.60|Prudul26B000915 site dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 R -753 -741 NNNGGAGAGACAG 7.7 7.1e-05 -9.550 4.148 6 6 PRUPE_6G006000|Prunus_persica.Prunus_persica_NCBIv2.60|PRUPE_6G006000 limit START_END D -233 199 . 0 0 0 0 Solyc11g072100.ITAG4.0|Solanum_lycopersicum.ITAG4.0.JGI|Solyc11g072100.ITAG4.0 limit START_END D -1501 199 . 0 0 0 0 ; ; Matrices ; matrix name ncol nrow pseudo Wmin Wmax Wrange ; 1 dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 13 4 1 -25.100 12.500 37.600 a:0.342 c:0.187 g:0.151 t:0.320 ; Number of sequences scanned 32 ; Sum of sequence lengths 51020 ; N residues 10767 ; Matches per matrix ; matrix name matches scored ; 1 dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2 41 101272 ; TOTAL 41 101272 ; Host name rsat ; Job started 2026-06-17.043243 ; Job done 2026-06-17.043252 ; Seconds 8.43 ; user 8.43 ; system 0.02 ; cuser 0.12 ; csystem 0.01