; matrix-scan -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/05/29/matrix-scan_2026-05-29.170051_JUe99a.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_2026-05-29.170051_hEt0kF.fasta -seq_format fasta -n score ; Slow counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/05/29/tmp_sequence_2026-05-29.170051_hEt0kF.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/05/29/matrix-scan_2026-05-29.170051_JUe99a.matrix ; Sequence format fasta ; Pseudo counts 1 ; Background model ; Method input ; Markov order 1 ; Strand undef ; Background pseudo-frequency 0.01 ; Residue probabilities ; a 0.34464 ; c 0.18339 ; g 0.14842 ; t 0.32356 ; 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_4g096340|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_4g096340 limit START_END D -1701 -1 . 0 0 0 0 BVRB_4g096340|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_4g096340 site oligos_6-8nt_m1 D -1527 -1512 GGTCCGACCNNNNNNN 7.6 3.0e-05 -10.399 4.516 1 1 BVRB_4g096340|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_4g096340 site oligos_6-8nt_m1 R -792 -777 GTCCGGCACCGTCACT 7.1 4.5e-05 -10.007 4.346 2 2 BVRB_4g096340|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_4g096340 site oligos_6-8nt_m1 D -593 -578 TGGTCGTCACGGTCAG 6.1 9.5e-05 -9.260 4.022 3 3 BVRB_4g096340|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_4g096340 site oligos_6-8nt_m1 D -247 -232 TCCCCGGCCCAGGGCA 6.0 1.0e-04 -9.180 3.987 4 4 T459_03445|Capsicum_annuum.ASM51225v2.60|T459_03445 limit START_END D -1701 -1 . 0 0 0 0 T459_03445|Capsicum_annuum.ASM51225v2.60|T459_03445 site oligos_6-8nt_m1 D -173 -158 GTTCTGTCCCACCTCA 8.2 1.9e-05 -10.874 4.723 1 1 T459_03445|Capsicum_annuum.ASM51225v2.60|T459_03445 site oligos_6-8nt_m1 D -23 -8 GGCCCGGCCCACTATG 8.1 2.1e-05 -10.793 4.688 2 2 T459_31204|Capsicum_annuum.ASM51225v2.60|T459_31204 limit START_END D -1701 -1 . 0 0 0 0 AUR62023693.v1.0|Chenopodium_quinoa.PI614886.392.v1.JGI|AUR62023693.v1.0 limit START_END D -1701 -1 . 0 0 0 0 Cla97C08G153070|Citrullus_lanatus.Cla97_v1.62|Cla97C08G153070 limit START_END D -1701 -1 . 0 0 0 0 MELO3C011439.2|Cucumis_melo.Melonv4.60|MELO3C011439.2 limit START_END D -1701 -1 . 0 0 0 0 Csa_6G366300|Cucumis_sativus.ASM407v2.60|Csa_6G366300 limit START_END D -1701 -1 . 0 0 0 0 HanXRQr2_Chr13g0574171|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr13g0574171 limit START_END D -1701 -1 . 0 0 0 0 HanXRQr2_Chr13g0574181|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr13g0574181 limit START_END D -1701 -1 . 0 0 0 0 gene-LSAT_8X33320|Lactuca_sativa.Lsat_Salinas_v7.60|gene-LSAT_8X33320 limit START_END D -1701 -1 . 0 0 0 0 gene25542|Medicago_truncatula.MtrunA17r50ANR.60|gene25542 limit START_END D -1701 -1 . 0 0 0 0 107761937|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107761937 limit START_END D -1701 -1 . 0 0 0 0 107761937|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107761937 site oligos_6-8nt_m1 R -330 -315 GGCCTGTCTCATGCCT 10.0 4.0e-06 -12.417 5.393 1 1 107761937|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107761937 site oligos_6-8nt_m1 D -576 -561 GGCCCGATCCATTACG 9.4 6.9e-06 -11.884 5.161 2 2 107761937|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107761937 site oligos_6-8nt_m1 R -325 -310 TGCTCGGCCTGTCTCA 8.9 1.1e-05 -11.458 4.976 3 3 107761937|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107761937 site oligos_6-8nt_m1 D -1313 -1298 TTCCCGAGACGTCCAC 8.0 2.2e-05 -10.712 4.652 4 4 107761937|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107761937 site oligos_6-8nt_m1 D -236 -221 GTCCAGTCCTCCCTCG 6.1 9.5e-05 -9.260 4.022 5 5 107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142 limit START_END D -1701 -1 . 0 0 0 0 107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142 site oligos_6-8nt_m1 D -1125 -1110 GCTCCAGCCCGCCCCG 12.0 6.2e-07 -14.298 6.210 1 1 107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142 site oligos_6-8nt_m1 D -1120 -1105 AGCCCGCCCCGTCTGT 11.2 1.3e-06 -13.516 5.870 2 2 107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142 site oligos_6-8nt_m1 R -170 -155 GGCCTGCCCCATGCTG 10.2 3.4e-06 -12.590 5.468 3 3 107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142 site oligos_6-8nt_m1 R -145 -130 GGCATGTCCTATGCCT 8.0 2.2e-05 -10.712 4.652 4 4 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 limit START_END D -1701 -1 . 0 0 0 0 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1511 -1496 GTCCCGTCCCATCCCG 18.3 2.9e-10 -21.963 9.538 1 1 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1363 -1348 GGGCCGTCCCGTCCCA 17.1 1.7e-09 -20.213 8.779 2 2 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1385 -1370 TCCCGGTCCCGTCCCG 16.7 2.8e-09 -19.691 8.552 3 3 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1368 -1353 GTCCCGTCCCATTCCG 16.6 3.3e-09 -19.532 8.482 4 4 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1390 -1375 GTCCCGTCCCGCGTCG 16.5 3.7e-09 -19.426 8.436 5 5 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1526 -1511 GTCATGTCCCGTCCCG 16.0 6.8e-09 -18.799 8.164 6 6 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1407 -1392 GTTCCGTCCCGTCCTG 15.9 7.7e-09 -18.685 8.115 7 7 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 D -1357 -1342 GGGACGGCCCGTCCCG 15.2 1.8e-08 -17.833 7.745 8 8 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -276 -261 GGCCTGTCCCATGCCG 15.1 2.1e-08 -17.701 7.688 9 9 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1531 -1516 GTCCCGTCCCGCCTAT 14.2 6.1e-08 -16.618 7.217 10 10 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1402 -1387 GTCGTGTTCCGTCCCG 13.6 1.2e-07 -15.962 6.932 11 11 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 D -1352 -1337 GGCCCGTCCCGTTGGA 13.3 1.6e-07 -15.665 6.803 12 12 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 D -1445 -1430 GGCCCATCCCGTTTAG 12.8 2.7e-07 -15.126 6.569 13 13 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1521 -1506 ATCCCGTCATGTCCCG 12.4 4.1e-07 -14.712 6.389 14 14 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1412 -1397 GTCCCGTCCTGTTTCA 12.3 4.5e-07 -14.605 6.343 15 15 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1358 -1343 GGGACGGGCCGTCCCG 12.3 4.5e-07 -14.605 6.343 16 16 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1516 -1501 GTCCCATCCCGTCATG 11.7 8.4e-07 -13.995 6.078 17 17 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1379 -1364 TTCCGGTCCCGGTCCC 10.8 2.0e-06 -13.143 5.708 18 18 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -251 -236 GGCATGTCCCATGCCT 10.4 2.8e-06 -12.782 5.551 19 19 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1506 -1491 CGTTTGTCCCGTCCCA 9.4 6.9e-06 -11.884 5.161 20 20 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1374 -1359 TCCCATTCCGGTCCCG 9.3 7.5e-06 -11.798 5.124 21 21 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1373 -1358 GTCCCATTCCGGTCCC 8.4 1.6e-05 -11.045 4.797 22 22 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1417 -1402 GTCCTGTTTCATTCCG 8.2 1.9e-05 -10.874 4.723 23 23 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1492 -1477 TGGCCATTTCGTCCCG 8.1 2.1e-05 -10.793 4.688 24 24 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 D -1300 -1285 TCTCCGATCCGTCCAT 8.1 2.1e-05 -10.793 4.688 25 25 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -246 -231 TGCTCGGCATGTCCCA 7.7 2.8e-05 -10.471 4.547 26 26 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1422 -1407 GTTTCATTCCGTCCCA 7.6 3.0e-05 -10.399 4.516 27 27 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 D -1362 -1347 GGGACGGGACGGCCCG 7.4 3.6e-05 -10.241 4.448 28 28 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -339 -324 GCCCCTTCTCTTCCAT 6.6 6.6e-05 -9.628 4.181 29 29 107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548 site oligos_6-8nt_m1 R -1397 -1382 CCCGCGTCGTGTTCCG 6.2 8.9e-05 -9.326 4.050 30 30 107812499|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107812499 limit START_END D -1701 -1 . 0 0 0 0 107812499|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107812499 site oligos_6-8nt_m1 R -314 -299 GGCCCGTCCCATGCCT 15.5 1.2e-08 -18.201 7.905 1 1 107812499|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107812499 site oligos_6-8nt_m1 R -309 -294 TGCTCGGCCCGTCCCA 13.6 1.2e-07 -15.962 6.932 2 2 107812499|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107812499 site oligos_6-8nt_m1 R -319 -304 GTCCCATGCCTTTACG 6.7 6.2e-05 -9.695 4.210 3 3 gene-LOC110794951|Spinacia_oleracea.GCF020520425.1.RefSeq|gene-LOC110794951 limit START_END D -1701 -1 . 0 0 0 0 gene-LOC110794951|Spinacia_oleracea.GCF020520425.1.RefSeq|gene-LOC110794951 site oligos_6-8nt_m1 R -323 -308 GCCCTGTTCGGTNNNN 7.5 3.3e-05 -10.312 4.478 1 1 ; ; Matrices ; matrix name ncol nrow pseudo Wmin Wmax Wrange ; 1 oligos_6-8nt_m1 16 4 1 -39.400 21.500 60.900 a:0.345 c:0.183 g:0.148 t:0.324 ; Number of sequences scanned 17 ; Sum of sequence lengths 27671 ; N residues 7120 ; Matches per matrix ; matrix name matches scored ; 1 oligos_6-8nt_m1 49 54832 ; TOTAL 49 54832 ; Host name rsat ; Job started 2026-05-29.170051 ; Job done 2026-05-29.170058 ; Seconds 6.19 ; user 6.19 ; system 0.03 ; cuser 0.08 ; csystem 0.02