; matrix-scan -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/06/17/matrix-scan_2026-06-17.030216_HfVrRg.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-3 -i $RSAT/public_html/tmp/www-data/2026/06/17/tmp_sequence_2026-06-17.030216_zt7bw6.fasta -seq_format fasta -n score ; Slow counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/06/17/tmp_sequence_2026-06-17.030216_zt7bw6.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/06/17/matrix-scan_2026-06-17.030216_HfVrRg.matrix ; Sequence format fasta ; Pseudo counts 1 ; Background model ; Method input ; Markov order 1 ; Strand undef ; Background pseudo-frequency 0.01 ; Residue probabilities ; a 0.34010 ; c 0.18996 ; g 0.15460 ; t 0.31534 ; Thresholds lower upper ; pval NA 0.001 ; 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 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 oligos_6-8nt_m2oligos_6-8nt_m2 D -1485 -1474 AACCATGCCTAG 8.1 7.3e-05 -9.532 4.140 1 1 AT3G13610|Arabidopsis_thaliana.TAIR10.60|F6'H1 site oligos_6-8nt_m2oligos_6-8nt_m2 D -1456 -1445 AACCATGCCTAG 8.1 7.3e-05 -9.532 4.140 2 2 AT3G13610|Arabidopsis_thaliana.TAIR10.60|F6'H1 site oligos_6-8nt_m2oligos_6-8nt_m2 R -507 -496 GTGCATGCAAGT 4.7 9.1e-04 -7.003 3.042 3 3 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 oligos_6-8nt_m2oligos_6-8nt_m2 D -137 -126 AAGCATGCCATA 9.4 1.2e-05 -11.317 4.915 1 1 GSBRNA2T00023848001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC05g39690D site oligos_6-8nt_m2oligos_6-8nt_m2 D -300 -289 AAACATGCCAGT 9.2 1.9e-05 -10.892 4.730 2 2 GSBRNA2T00023848001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC05g39690D site oligos_6-8nt_m2oligos_6-8nt_m2 D -882 -871 GTCCATGCCTCT 7.8 9.0e-05 -9.320 4.048 3 3 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 oligos_6-8nt_m2oligos_6-8nt_m2 D -295 -284 AAACATGCCAGT 9.2 1.9e-05 -10.892 4.730 1 1 GSBRNA2T00104708001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA05g25780D site oligos_6-8nt_m2oligos_6-8nt_m2 D -137 -126 AAGCATGCCATC 8.7 3.9e-05 -10.157 4.411 2 2 GSBRNA2T00104708001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA05g25780D site oligos_6-8nt_m2oligos_6-8nt_m2 D -890 -879 GTCCATGCCTCT 7.8 9.0e-05 -9.320 4.048 3 3 GSBRNA2T00104708001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA05g25780D site oligos_6-8nt_m2oligos_6-8nt_m2 R -1061 -1050 TTCCACGCCTCA 5.1 6.1e-04 -7.401 3.214 4 4 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 oligos_6-8nt_m2oligos_6-8nt_m2 D -1247 -1236 AACCATGCCCAG 7.0 1.3e-04 -8.938 3.882 1 1 GSBRNA2T00123637001|Brassica_napus.AST_PRJEB5043_v1.60|BnaC03g38030D site oligos_6-8nt_m2oligos_6-8nt_m2 D -592 -581 AACCAAGCCAAT 4.9 7.4e-04 -7.203 3.128 2 2 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 oligos_6-8nt_m2oligos_6-8nt_m2 D -991 -980 AACCATGCCCAG 7.0 1.3e-04 -8.938 3.882 1 1 GSBRNA2T00137685001|Brassica_napus.AST_PRJEB5043_v1.60|BnaA03g32900D site oligos_6-8nt_m2oligos_6-8nt_m2 D -108 -97 TGTCATTCCTTT 4.9 7.4e-04 -7.203 3.128 2 2 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 oligos_6-8nt_m2oligos_6-8nt_m2 D -108 -97 TGTCATTCCTTT 4.9 7.4e-04 -7.203 3.128 1 1 GLYMA_07G124400|Glycine_max.Glycine_max_v2.1.60|GLYMA_07G124400 limit START_END D -1501 199 . 0 0 0 0 GLYMA_07G124400|Glycine_max.Glycine_max_v2.1.60|GLYMA_07G124400 site oligos_6-8nt_m2oligos_6-8nt_m2 R -18 -7 ATTCATGCCGGG 9.2 1.9e-05 -10.892 4.730 1 1 GLYMA_07G124400|Glycine_max.Glycine_max_v2.1.60|GLYMA_07G124400 site oligos_6-8nt_m2oligos_6-8nt_m2 R -316 -305 ATTCATCCCATT 7.2 1.2e-04 -9.012 3.914 2 2 GLYMA_07G124400|Glycine_max.Glycine_max_v2.1.60|GLYMA_07G124400 site oligos_6-8nt_m2oligos_6-8nt_m2 D -262 -251 TTGCATGCCCCA 6.3 1.9e-04 -8.576 3.724 3 3 GLYMA_07G124400|Glycine_max.Glycine_max_v2.1.60|GLYMA_07G124400 site oligos_6-8nt_m2oligos_6-8nt_m2 R -98 -87 TAACTTGCCTTA 4.8 8.3e-04 -7.096 3.082 4 4 GLYMA_07G124400|Glycine_max.Glycine_max_v2.1.60|GLYMA_07G124400 site oligos_6-8nt_m2oligos_6-8nt_m2 R -804 -793 GGTCATGCTATC 4.7 9.1e-04 -7.003 3.042 5 5 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 oligos_6-8nt_m2oligos_6-8nt_m2 D -430 -419 GGACATGCCGGA 7.6 1.0e-04 -9.205 3.998 1 1 gene-Lalb_Chr13g0290931|Lupinus_albus.CNRS_Lalb_10.GCA_009771035.1.NCBI|gene-Lalb_Chr13g0290931 site oligos_6-8nt_m2oligos_6-8nt_m2 D -164 -153 TAACTTGCCATT 6.1 2.2e-04 -8.418 3.656 2 2 gene-Lalb_Chr13g0290931|Lupinus_albus.CNRS_Lalb_10.GCA_009771035.1.NCBI|gene-Lalb_Chr13g0290931 site oligos_6-8nt_m2oligos_6-8nt_m2 D -578 -567 NNNNNNGCCGTT 5.9 2.6e-04 -8.241 3.579 3 3 gene-Lalb_Chr13g0290931|Lupinus_albus.CNRS_Lalb_10.GCA_009771035.1.NCBI|gene-Lalb_Chr13g0290931 site oligos_6-8nt_m2oligos_6-8nt_m2 D -876 -865 AAACATGACATT 5.2 5.6e-04 -7.493 3.254 4 4 107763182|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107763182 limit START_END D -1501 199 . 0 0 0 0 107763182|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107763182 site oligos_6-8nt_m2oligos_6-8nt_m2 D -490 -479 AAACATGCCAAG 8.5 4.9e-05 -9.918 4.307 1 1 107763182|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107763182 site oligos_6-8nt_m2oligos_6-8nt_m2 R -754 -743 ACACTTGCCATT 6.1 2.2e-04 -8.418 3.656 2 2 107763182|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107763182 site oligos_6-8nt_m2oligos_6-8nt_m2 R 105 116 TGACATTCCATG 4.9 7.4e-04 -7.203 3.128 3 3 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 oligos_6-8nt_m2oligos_6-8nt_m2 D 8 19 ACCCATACCATT 5.5 4.1e-04 -7.810 3.392 1 1 107785648|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107785648 site oligos_6-8nt_m2oligos_6-8nt_m2 R -132 -121 AATCATGCGGCA 5.0 6.8e-04 -7.287 3.165 2 2 107796566|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107796566 limit START_END D -1501 199 . 0 0 0 0 107796566|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107796566 site oligos_6-8nt_m2oligos_6-8nt_m2 R -44 -33 TGGCATGCCATG 8.5 4.9e-05 -9.918 4.307 1 1 107796566|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107796566 site oligos_6-8nt_m2oligos_6-8nt_m2 D -42 -31 TGGCATGCCAAT 8.2 6.6e-05 -9.619 4.177 2 2 107796566|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107796566 site oligos_6-8nt_m2oligos_6-8nt_m2 R 139 150 CTCCATGCCCTT 7.3 1.2e-04 -9.058 3.934 3 3 107796566|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107796566 site oligos_6-8nt_m2oligos_6-8nt_m2 D -546 -535 ATACATGCTAAT 5.7 3.3e-04 -8.026 3.486 4 4 107796566|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107796566 site oligos_6-8nt_m2oligos_6-8nt_m2 R -1137 -1126 TCTCACGCCCAG 5.6 3.6e-04 -7.930 3.444 5 5 107796566|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107796566 site oligos_6-8nt_m2oligos_6-8nt_m2 D -47 -36 TTTCATGGCATG 5.6 3.6e-04 -7.930 3.444 6 6 107796566|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107796566 site oligos_6-8nt_m2oligos_6-8nt_m2 R -828 -817 GATCATGCATGT 4.7 9.1e-04 -7.003 3.042 7 7 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 oligos_6-8nt_m2oligos_6-8nt_m2 R -987 -976 TTTCATTCCTTT 5.1 6.1e-04 -7.401 3.214 1 1 107787976|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107787976 site oligos_6-8nt_m2oligos_6-8nt_m2 D -318 -307 TGTCATGCGCGT 5.1 6.1e-04 -7.401 3.214 2 2 107787976|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107787976 site oligos_6-8nt_m2oligos_6-8nt_m2 R -429 -418 TTTCATCCCCTA 4.7 9.1e-04 -7.003 3.042 3 3 Prudul26B000915|Prunus_dulcis.ALMONDv2.60|Prudul26B000915 limit START_END D -773 199 . 0 0 0 0 Prudul26B000915|Prunus_dulcis.ALMONDv2.60|Prudul26B000915 site oligos_6-8nt_m2oligos_6-8nt_m2 D -19 -8 AATCATACCAGA 5.7 3.3e-04 -8.026 3.486 1 1 Prudul26B000915|Prunus_dulcis.ALMONDv2.60|Prudul26B000915 site oligos_6-8nt_m2oligos_6-8nt_m2 D -179 -168 AAGCATGCTAAT 5.2 5.6e-04 -7.493 3.254 2 2 PRUPE_6G006000|Prunus_persica.Prunus_persica_NCBIv2.60|PRUPE_6G006000 limit START_END D -233 199 . 0 0 0 0 PRUPE_6G006000|Prunus_persica.Prunus_persica_NCBIv2.60|PRUPE_6G006000 site oligos_6-8nt_m2oligos_6-8nt_m2 D 77 88 AAGCATGCTAAT 5.2 5.6e-04 -7.493 3.254 1 1 Solyc11g072100.ITAG4.0|Solanum_lycopersicum.ITAG4.0.JGI|Solyc11g072100.ITAG4.0 limit START_END D -1501 199 . 0 0 0 0 Solyc11g072100.ITAG4.0|Solanum_lycopersicum.ITAG4.0.JGI|Solyc11g072100.ITAG4.0 site oligos_6-8nt_m2oligos_6-8nt_m2 R -963 -952 AAACATCCCAGT 5.9 2.6e-04 -8.241 3.579 1 1 Solyc11g072100.ITAG4.0|Solanum_lycopersicum.ITAG4.0.JGI|Solyc11g072100.ITAG4.0 site oligos_6-8nt_m2oligos_6-8nt_m2 D -1273 -1262 GATCATGACATA 5.5 4.1e-04 -7.810 3.392 2 2 ; ; Matrices ; matrix name ncol nrow pseudo Wmin Wmax Wrange ; 1 oligos_6-8nt_m2oligos_6-8nt_m2 12 4 1 -22.600 10.900 33.500 a:0.340 c:0.190 g:0.155 t:0.315 ; Number of sequences scanned 15 ; Sum of sequence lengths 23349 ; N residues 3647 ; Matches per matrix ; matrix name matches scored ; 1 oligos_6-8nt_m2oligos_6-8nt_m2 44 46368 ; TOTAL 44 46368 ; Host name rsat ; Job started 2026-06-17.030216 ; Job done 2026-06-17.030220 ; Seconds 3.83 ; user 3.83 ; system 0.02 ; cuser 0.08 ; csystem 0.03