; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.103950_JL2cOA.matrix -pseudo 1 -decimals 1 -2str -origin end -bgfile $RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.60/oligo-frequencies/2nt_upstream_Arabidopsis_thaliana.TAIR10.60-ovlp-1str.freq -bg_pseudo 0.01 -return limits -return pval -uth pval 0.001 -i $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.103950_cDMsDL.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.103950_cDMsDL.fasta ; bg $RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.60/oligo-frequencies/2nt_upstream_Arabidopsis_thaliana.TAIR10.60-ovlp-1str.freq ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.103950_JL2cOA.matrix ; Sequence format fasta ; Pseudo counts 1 ; Background model ; Method file ; Markov order 1 ; Strand sensitive ; Background pseudo-frequency 0.01 ; Residue probabilities ; a 0.32476 ; c 0.17479 ; g 0.17640 ; t 0.32405 ; Thresholds lower upper ; pval NA 0.001 ; 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 AT1G69770 limit START_END D -500 -1 . 0 0 0 0 AT5G49160 limit START_END D -500 -1 . 0 0 0 0 AT4G12620 limit START_END D -500 -1 . 0 0 0 0 AT1G67320 limit START_END D -500 -1 . 0 0 0 0 AT3G54650 limit START_END D -500 -1 . 0 0 0 0 AT2G31270 limit START_END D -500 -1 . 0 0 0 0 AT2G41460 limit START_END D -500 -1 . 0 0 0 0 AT4G02070 limit START_END D -500 -1 . 0 0 0 0 AT5G14530 limit START_END D -500 -1 . 0 0 0 0 AT2G46380 limit START_END D -500 -1 . 0 0 0 0 AT2G29680 limit START_END D -500 -1 . 0 0 0 0 AT3G12280 limit START_END D -500 -1 . 0 0 0 0 AT3G18630 limit START_END D -500 -1 . 0 0 0 0 AT1G68200 limit START_END D -500 -1 . 0 0 0 0 AT1G67500 limit START_END D -500 -1 . 0 0 0 0 AT1G67630 limit START_END D -500 -1 . 0 0 0 0 AT1G49540 limit START_END D -500 -1 . 0 0 0 0 AT2G24490 limit START_END D -500 -1 . 0 0 0 0 AT2G16440 limit START_END D -500 -1 . 0 0 0 0 AT2G21790 limit START_END D -500 -1 . 0 0 0 0 AT3G25100 limit START_END D -500 -1 . 0 0 0 0 AT1G08130 limit START_END D -500 -1 . 0 0 0 0 AT1G07270 limit START_END D -500 -1 . 0 0 0 0 AT1G07370 limit START_END D -500 -1 . 0 0 0 0 AT1G69770 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -486 -479 ATTCCCAC 6.3 3.3e-04 -8.016 3.481 AT1G69770 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -262 -255 ATTCCCGG 6.6 2.7e-04 -8.217 3.569 AT1G69770 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -195 -188 CTTCCCAC 4.8 9.2e-04 -6.991 3.036 AT1G69770 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -78 -71 TCTCTCGC 4.9 9.2e-04 -6.991 3.036 AT1G67320 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -363 -356 TTACCCCC 4.8 9.2e-04 -6.991 3.036 AT2G46380 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -375 -368 TTACCTGC 5.0 8.1e-04 -7.118 3.092 AT2G46380 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -282 -275 TTTCCCTC 6.6 2.7e-04 -8.217 3.569 AT3G12280 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -76 -69 TTTCCCGC 9.9 6.1e-06 -12.007 5.215 AT1G68200 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -220 -213 TATCCCTC 4.9 8.1e-04 -7.118 3.092 AT1G49540 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -37 -30 ATTCCCTC 6.2 3.5e-04 -7.958 3.456 AT2G24490 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -60 -53 TTACTCGC 5.3 4.9e-04 -7.621 3.310 AT2G16440 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -230 -223 GTTCCCTC 4.8 9.2e-04 -6.991 3.036 AT2G16440 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -17 -10 GTCCCCGC 5.9 3.7e-04 -7.902 3.432 AT2G21790 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -222 -215 TGTTCCGC 4.9 8.1e-04 -7.118 3.092 AT2G21790 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -37 -30 TTACCCGC 8.2 2.0e-05 -10.820 4.699 AT3G25100 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -61 -54 TTTCCCTC 6.6 2.7e-04 -8.217 3.569 AT3G25100 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -53 -46 TTTCCCTC 6.6 2.7e-04 -8.217 3.569 AT1G08130 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -21 -14 TAGCCCGC 6.0 3.7e-04 -7.902 3.432 AT1G07270 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -130 -123 GTTCACGC 5.4 4.3e-04 -7.752 3.367 AT1G07270 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -42 -35 TCTCCCGC 7.8 3.1e-05 -10.382 4.509 AT1G07270 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -14 -7 TTTCCCGC 9.9 6.1e-06 -12.007 5.215 AT1G69770 site 5015_E2Fb_Athamap_20091028_ R -486 -479 ATTCCCAC 6.2 3.3e-04 -8.016 3.481 AT1G69770 site 5015_E2Fb_Athamap_20091028_ R -262 -255 ATTCCCGG 6.4 2.8e-04 -8.181 3.553 AT1G69770 site 5015_E2Fb_Athamap_20091028_ R -195 -188 CTTCCCAC 4.7 9.0e-04 -7.013 3.046 AT1G69770 site 5015_E2Fb_Athamap_20091028_ R -78 -71 TCTCTCGC 4.8 7.7e-04 -7.169 3.114 AT5G49160 site 5015_E2Fb_Athamap_20091028_ D -17 -10 TTTAGCGC 4.6 9.0e-04 -7.013 3.046 AT1G67320 site 5015_E2Fb_Athamap_20091028_ R -363 -356 TTACCCCC 4.8 8.6e-04 -7.059 3.066 AT2G46380 site 5015_E2Fb_Athamap_20091028_ R -375 -368 TTACCTGC 4.9 6.5e-04 -7.339 3.187 AT2G46380 site 5015_E2Fb_Athamap_20091028_ D -282 -275 TTTCCCTC 6.8 2.2e-04 -8.422 3.658 AT3G12280 site 5015_E2Fb_Athamap_20091028_ D -76 -69 TTTCCCGC 10.4 6.1e-06 -12.007 5.215 AT1G68200 site 5015_E2Fb_Athamap_20091028_ D -220 -213 TATCCCTC 4.8 7.7e-04 -7.169 3.114 AT1G49540 site 5015_E2Fb_Athamap_20091028_ D -37 -30 ATTCCCTC 6.1 3.5e-04 -7.958 3.456 AT2G24490 site 5015_E2Fb_Athamap_20091028_ R -60 -53 TTACTCGC 5.2 4.8e-04 -7.642 3.319 AT2G16440 site 5015_E2Fb_Athamap_20091028_ R -230 -223 GTTCCCTC 4.7 8.6e-04 -7.059 3.066 AT2G16440 site 5015_E2Fb_Athamap_20091028_ D -17 -10 GTCCCCGC 5.8 3.7e-04 -7.902 3.432 AT2G21790 site 5015_E2Fb_Athamap_20091028_ R -222 -215 TGTTCCGC 4.8 7.7e-04 -7.169 3.114 AT2G21790 site 5015_E2Fb_Athamap_20091028_ D -37 -30 TTACCCGC 8.4 1.8e-05 -10.925 4.745 AT3G25100 site 5015_E2Fb_Athamap_20091028_ D -61 -54 TTTCCCTC 6.8 2.2e-04 -8.422 3.658 AT3G25100 site 5015_E2Fb_Athamap_20091028_ D -53 -46 TTTCCCTC 6.8 2.2e-04 -8.422 3.658 AT1G08130 site 5015_E2Fb_Athamap_20091028_ D -21 -14 TAGCCCGC 5.9 3.5e-04 -7.958 3.456 AT1G07270 site 5015_E2Fb_Athamap_20091028_ R -130 -123 GTTCACGC 5.2 4.8e-04 -7.642 3.319 AT1G07270 site 5015_E2Fb_Athamap_20091028_ R -42 -35 TCTCCCGC 8.0 3.2e-05 -10.350 4.495 AT1G07270 site 5015_E2Fb_Athamap_20091028_ D -14 -7 TTTCCCGC 10.4 6.1e-06 -12.007 5.215 AT1G69770 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -266 -256 TTCCCGGGGTA 5.2 5.6e-04 -7.488 3.252 AT1G69770 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -82 -72 CTCTCGCTATA 5.2 5.2e-04 -7.562 3.284 AT1G69770 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -80 -70 TTCTCTCGCTA 4.5 9.6e-04 -6.949 3.018 AT5G49160 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -487 -477 ATGCCGCTATT 5.9 3.0e-04 -8.112 3.523 AT5G49160 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -16 -6 TTAGCGCCGTT 5.1 5.6e-04 -7.488 3.252 AT2G31270 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -11 -1 TTCCCGCGAAA 11.0 1.6e-06 -13.346 5.796 AT2G46380 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -379 -369 TACCTGCCTAT 5.4 4.4e-04 -7.729 3.357 AT3G12280 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -327 -317 TTCGCGGTCTA 6.4 2.0e-04 -8.517 3.699 AT3G12280 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -136 -126 TATCCGCGGAT 4.6 8.8e-04 -7.036 3.056 AT3G12280 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -75 -65 TTCCCGCGTGA 6.6 1.7e-04 -8.680 3.770 AT3G18630 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -447 -437 TTGCCGACATA 5.3 4.7e-04 -7.663 3.328 AT1G68200 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -219 -209 ATCCCTCCAAA 6.9 1.3e-04 -8.948 3.886 AT1G67630 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -349 -339 TTCCCTACAAA 5.0 6.2e-04 -7.386 3.208 AT1G49540 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -307 -297 TGTCCGCGATA 5.5 4.1e-04 -7.799 3.387 AT2G16440 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -39 -29 TTGGCGCCATT 6.7 1.6e-04 -8.740 3.796 AT2G16440 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -38 -28 ATGGCGCCAAA 6.2 2.4e-04 -8.335 3.620 AT2G16440 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -16 -6 TCCCCGCCTAA 7.4 9.2e-05 -9.294 4.036 AT2G21790 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -36 -26 TACCCGCCATT 10.6 3.0e-06 -12.717 5.523 AT1G08130 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -434 -424 TACGCGCTCAT 8.9 1.4e-05 -11.176 4.854 AT1G07270 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -134 -124 TTCACGCTGAA 4.9 6.8e-04 -7.293 3.167 AT1G07270 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -46 -36 CTCCCGCCTTT 6.3 2.2e-04 -8.422 3.658 AT1G07270 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -30 -20 ATCGCGACATT 6.0 2.8e-04 -8.181 3.553 AT1G07270 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -13 -3 TTCCCGCTACT 8.3 3.0e-05 -10.414 4.523 AT1G07370 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -345 -335 TACGTGCGAAT 5.7 3.6e-04 -7.929 3.444 AT1G07370 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -286 -276 TTCCCATCCAT 4.7 8.1e-04 -7.118 3.092 AT1G07370 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -153 -143 AACACGCGAAT 5.6 3.8e-04 -7.875 3.420 ; ; Matrices ; matrix name ncol nrow pseudo Wmin Wmax Wrange ; 1 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ 8 4 0 -11.100 10.100 21.200 a:0.325 c:0.175 g:0.176 t:0.324 ; 2 5015_E2Fb_Athamap_20091028_ 8 4 0 -12.900 10.500 23.400 a:0.325 c:0.175 g:0.176 t:0.324 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 11 4 0 -19.800 12.300 32.100 a:0.325 c:0.175 g:0.176 t:0.324 ; Number of sequences scanned 24 ; Sum of sequence lengths 12000 ; N residues 0 ; Matches per matrix ; matrix name matches scored ; 1 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ 21 0 ; 2 5015_E2Fb_Athamap_20091028_ 22 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 26 0 ; TOTAL 69 0 ; Host name rsat ; Job started 2026-08-17.103951 ; Job done 2026-08-17.103952 ; Seconds 0.48 ; user 0.48 ; system 0.03 ; cuser 0.83 ; csystem 0.09