; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.104053_r2NUal.matrix -pseudo 1 -decimals 1 -2str -origin end -bgfile $RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.60/oligo-frequencies/2nt_upstream-noorf_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_2026-08-17.104053_fk9ifL.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.104053_fk9ifL.fasta ; bg $RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.60/oligo-frequencies/2nt_upstream-noorf_Arabidopsis_thaliana.TAIR10.60-ovlp-1str.freq ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.104053_r2NUal.matrix ; Sequence format fasta ; Pseudo counts 1 ; Background model ; Method file ; Markov order 1 ; Strand sensitive ; Background pseudo-frequency 0.01 ; Residue probabilities ; a 0.34589 ; c 0.15671 ; g 0.15366 ; t 0.34374 ; 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 6.5 2.7e-04 -8.217 3.569 AT1G69770 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -262 -255 ATTCCCGG 6.6 2.6e-04 -8.255 3.585 AT1G69770 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -195 -188 CTTCCCAC 5.1 6.7e-04 -7.308 3.174 AT1G69770 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -78 -71 TCTCTCGC 5.4 4.2e-04 -7.775 3.377 AT5G49160 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -17 -10 TTTAGCGC 4.8 8.8e-04 -7.036 3.056 AT1G67320 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -363 -356 TTACCCCC 4.8 8.8e-04 -7.036 3.056 AT4G02070 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -370 -363 ACTCTCGC 5.0 8.0e-04 -7.131 3.097 AT2G46380 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -375 -368 TTACCTGC 5.2 5.9e-04 -7.435 3.229 AT2G46380 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -282 -275 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 AT2G46380 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -83 -76 TCTCCCTC 4.9 8.0e-04 -7.131 3.097 AT3G12280 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -76 -69 TTTCCCGC 10.2 4.7e-06 -12.268 5.328 AT1G68200 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -220 -213 TATCCCTC 5.2 5.9e-04 -7.435 3.229 AT1G68200 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -133 -126 TCTCCAGC 5.1 6.7e-04 -7.308 3.174 AT1G49540 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -303 -296 ATGTCCGC 4.8 9.5e-04 -6.959 3.022 AT1G49540 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -37 -30 ATTCCCTC 6.6 2.6e-04 -8.255 3.585 AT2G24490 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -60 -53 TTACTCGC 5.6 3.5e-04 -7.958 3.456 AT2G16440 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -230 -223 GTTCCCTC 5.2 6.7e-04 -7.308 3.174 AT2G16440 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -17 -10 GTCCCCGC 6.2 2.9e-04 -8.146 3.538 AT2G21790 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -222 -215 TGTTCCGC 5.1 6.7e-04 -7.308 3.174 AT2G21790 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -37 -30 TTACCCGC 8.3 1.8e-05 -10.925 4.745 AT3G25100 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -61 -54 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 AT3G25100 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -53 -46 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 AT1G08130 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -21 -14 TAGCCCGC 6.3 2.9e-04 -8.146 3.538 AT1G07270 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -484 -477 TCTCCCTC 4.9 8.0e-04 -7.131 3.097 AT1G07270 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -130 -123 GTTCACGC 5.6 3.5e-04 -7.958 3.456 AT1G07270 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -42 -35 TCTCCCGC 8.2 1.9e-05 -10.871 4.721 AT1G07270 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -14 -7 TTTCCCGC 10.2 4.7e-06 -12.268 5.328 AT1G69770 site 5015_E2Fb_Athamap_20091028_ R -486 -479 ATTCCCAC 6.3 2.7e-04 -8.217 3.569 AT1G69770 site 5015_E2Fb_Athamap_20091028_ R -262 -255 ATTCCCGG 6.5 2.5e-04 -8.294 3.602 AT1G69770 site 5015_E2Fb_Athamap_20091028_ R -195 -188 CTTCCCAC 5.0 6.9e-04 -7.279 3.161 AT1G69770 site 5015_E2Fb_Athamap_20091028_ R -78 -71 TCTCTCGC 5.4 4.4e-04 -7.729 3.357 AT5G49160 site 5015_E2Fb_Athamap_20091028_ D -17 -10 TTTAGCGC 4.7 7.9e-04 -7.143 3.102 AT1G67320 site 5015_E2Fb_Athamap_20091028_ R -363 -356 TTACCCCC 4.7 7.9e-04 -7.143 3.102 AT4G02070 site 5015_E2Fb_Athamap_20091028_ D -370 -363 ACTCTCGC 4.5 9.4e-04 -6.970 3.027 AT2G46380 site 5015_E2Fb_Athamap_20091028_ R -375 -368 TTACCTGC 5.1 5.8e-04 -7.452 3.237 AT2G46380 site 5015_E2Fb_Athamap_20091028_ D -282 -275 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 AT2G46380 site 5015_E2Fb_Athamap_20091028_ D -83 -76 TCTCCCTC 4.8 7.5e-04 -7.195 3.125 AT3G12280 site 5015_E2Fb_Athamap_20091028_ D -76 -69 TTTCCCGC 10.7 4.7e-06 -12.268 5.328 AT1G68200 site 5015_E2Fb_Athamap_20091028_ D -220 -213 TATCCCTC 5.1 5.8e-04 -7.452 3.237 AT1G68200 site 5015_E2Fb_Athamap_20091028_ D -133 -126 TCTCCAGC 5.0 6.5e-04 -7.339 3.187 AT1G49540 site 5015_E2Fb_Athamap_20091028_ D -37 -30 ATTCCCTC 6.4 2.6e-04 -8.255 3.585 AT2G24490 site 5015_E2Fb_Athamap_20091028_ R -60 -53 TTACTCGC 5.5 3.6e-04 -7.929 3.444 AT2G16440 site 5015_E2Fb_Athamap_20091028_ R -230 -223 GTTCCCTC 5.0 6.5e-04 -7.339 3.187 AT2G16440 site 5015_E2Fb_Athamap_20091028_ D -17 -10 GTCCCCGC 6.0 2.9e-04 -8.146 3.538 AT2G21790 site 5015_E2Fb_Athamap_20091028_ R -222 -215 TGTTCCGC 5.1 6.5e-04 -7.339 3.187 AT2G21790 site 5015_E2Fb_Athamap_20091028_ D -37 -30 TTACCCGC 8.5 1.8e-05 -10.925 4.745 AT3G25100 site 5015_E2Fb_Athamap_20091028_ D -61 -54 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 AT3G25100 site 5015_E2Fb_Athamap_20091028_ D -53 -46 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 AT1G08130 site 5015_E2Fb_Athamap_20091028_ D -21 -14 TAGCCCGC 6.2 2.8e-04 -8.181 3.553 AT1G07270 site 5015_E2Fb_Athamap_20091028_ R -484 -477 TCTCCCTC 4.8 7.5e-04 -7.195 3.125 AT1G07270 site 5015_E2Fb_Athamap_20091028_ R -130 -123 GTTCACGC 5.5 3.6e-04 -7.929 3.444 AT1G07270 site 5015_E2Fb_Athamap_20091028_ R -42 -35 TCTCCCGC 8.4 2.1e-05 -10.771 4.678 AT1G07270 site 5015_E2Fb_Athamap_20091028_ D -14 -7 TTTCCCGC 10.7 4.7e-06 -12.268 5.328 AT1G69770 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -266 -256 TTCCCGGGGTA 5.1 5.4e-04 -7.524 3.268 AT1G69770 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -82 -72 CTCTCGCTATA 5.5 3.9e-04 -7.849 3.409 AT1G69770 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -80 -70 TTCTCTCGCTA 5.1 5.4e-04 -7.524 3.268 AT5G49160 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -487 -477 ATGCCGCTATT 5.9 2.9e-04 -8.146 3.538 AT5G49160 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -16 -6 TTAGCGCCGTT 5.2 5.0e-04 -7.601 3.301 AT2G31270 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -11 -1 TTCCCGCGAAA 11.3 1.1e-06 -13.720 5.959 AT2G46380 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -379 -369 TACCTGCCTAT 5.6 3.6e-04 -7.929 3.444 AT3G12280 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -327 -317 TTCGCGGTCTA 6.5 1.8e-04 -8.623 3.745 AT3G12280 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -136 -126 TATCCGCGGAT 4.7 7.7e-04 -7.169 3.114 AT3G12280 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -75 -65 TTCCCGCGTGA 7.0 1.2e-04 -9.028 3.921 AT3G18630 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -447 -437 TTGCCGACATA 5.3 4.6e-04 -7.684 3.337 AT1G68200 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -219 -209 ATCCCTCCAAA 7.2 1.0e-04 -9.210 4.000 AT1G67630 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -349 -339 TTCCCTACAAA 5.0 6.0e-04 -7.419 3.222 AT1G67630 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -240 -230 ATCTAGCCAAA 4.5 9.1e-04 -7.002 3.041 AT1G49540 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -307 -297 TGTCCGCGATA 5.6 3.6e-04 -7.929 3.444 AT2G24490 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -64 -54 TACTCGCGGTT 4.6 8.3e-04 -7.094 3.081 AT2G16440 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -39 -29 TTGGCGCCATT 6.8 1.4e-04 -8.874 3.854 AT2G16440 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -38 -28 ATGGCGCCAAA 6.3 2.1e-04 -8.468 3.678 AT2G16440 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -16 -6 TCCCCGCCTAA 7.6 6.6e-05 -9.626 4.180 AT2G21790 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -36 -26 TACCCGCCATT 10.7 2.8e-06 -12.786 5.553 AT1G08130 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -434 -424 TACGCGCTCAT 9.2 1.0e-05 -11.513 5.000 AT1G07270 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -134 -124 TTCACGCTGAA 5.2 5.0e-04 -7.601 3.301 AT1G07270 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -46 -36 CTCCCGCCTTT 6.7 1.5e-04 -8.805 3.824 AT1G07270 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -30 -20 ATCGCGACATT 6.3 2.3e-04 -8.377 3.638 AT1G07270 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -13 -3 TTCCCGCTACT 8.5 2.4e-05 -10.637 4.620 AT1G07370 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -345 -335 TACGTGCGAAT 5.8 3.1e-04 -8.079 3.509 AT1G07370 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -286 -276 TTCCCATCCAT 4.9 6.5e-04 -7.339 3.187 AT1G07370 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -153 -143 AACACGCGAAT 5.8 3.1e-04 -8.079 3.509 ; ; Matrices ; matrix name ncol nrow pseudo Wmin Wmax Wrange ; 1 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ 8 4 0 -11.100 10.500 21.600 a:0.346 c:0.157 g:0.154 t:0.344 ; 2 5015_E2Fb_Athamap_20091028_ 8 4 0 -12.900 10.900 23.800 a:0.346 c:0.157 g:0.154 t:0.344 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 11 4 0 -19.800 12.800 32.600 a:0.346 c:0.157 g:0.154 t:0.344 ; 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_ 27 0 ; 2 5015_E2Fb_Athamap_20091028_ 26 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 28 0 ; TOTAL 81 0 ; Host name rsat ; Job started 2026-08-17.104053 ; Job done 2026-08-17.104054 ; Seconds 0.46 ; user 0.46 ; system 0.04 ; cuser 0.78 ; csystem 0.07