; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.170345_FNhhOe.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_2026-08-17.170345_aruAFS.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; bg $RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.60/oligo-frequencies/2nt_upstream-noorf_Arabidopsis_thaliana.TAIR10.60-ovlp-1str.freq ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.170345_aruAFS.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.170345_FNhhOe.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 AT3G09595|AT3G09595 limit START_END D -500 -1 . 0 0 0 0 AT3G14130|GLO4 limit START_END D -500 -1 . 0 0 0 0 AT3G01570|AT3G01570 limit START_END D -500 -1 . 0 0 0 0 AT5G58280|AT5G58280 limit START_END D -500 -1 . 0 0 0 0 AT5G38710|POX2 limit START_END D -500 -1 . 0 0 0 0 AT1G74370|AT1G74370 limit START_END D -500 -1 . 0 0 0 0 AT3G04560|AT3G04560 limit START_END D -500 -1 . 0 0 0 0 AT1G57140|AT1G57140 limit START_END D -500 -1 . 0 0 0 0 AT2G15460|AT2G15460 limit START_END D -500 -1 . 0 0 0 0 AT1G27060|AT1G27060 limit START_END D -500 -1 . 0 0 0 0 AT4G31290|AT4G31290 limit START_END D -500 -1 . 0 0 0 0 AT3G27831|AT3G27831 limit START_END D -500 -1 . 0 0 0 0 AT5G06650|GIS2 limit START_END D -500 -1 . 0 0 0 0 AT1G17690|NOF1 limit START_END D -500 -1 . 0 0 0 0 AT4G37390|YDK1 limit START_END D -500 -1 . 0 0 0 0 AT1G70890|MLP43 limit START_END D -500 -1 . 0 0 0 0 AT1G57870|ATSK42 limit START_END D -500 -1 . 0 0 0 0 AT1G28200|FIP1 limit START_END D -500 -1 . 0 0 0 0 AT4G24060|DOF4.6 limit START_END D -500 -1 . 0 0 0 0 AT4G29350|PRO2 limit START_END D -500 -1 . 0 0 0 0 AT2G32020|AT2G32020 limit START_END D -500 -1 . 0 0 0 0 AT4G14550|IAA14 limit START_END D -500 -1 . 0 0 0 0 AT3G49668|AT3G49668 limit START_END D -500 -1 . 0 0 0 0 AT5G09900|EMB2107 limit START_END D -500 -1 . 0 0 0 0 AT3G09595|AT3G09595 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -329 -322 TTGTCCGC 5.1 6.7e-04 -7.308 3.174 AT3G09595|AT3G09595 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -180 -173 TTGGCCGC 5.1 7.4e-04 -7.209 3.131 AT3G09595|AT3G09595 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -140 -133 CTTGCCGC 5.6 3.5e-04 -7.958 3.456 AT3G14130|GLO4 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -294 -287 TTCCCCGT 4.9 8.0e-04 -7.131 3.097 AT3G14130|GLO4 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -278 -271 TGTTCCGC 5.1 6.7e-04 -7.308 3.174 AT3G14130|GLO4 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -54 -47 TTGCCCAC 4.7 9.5e-04 -6.959 3.022 AT5G58280|AT5G58280 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -408 -401 CTGCCCGC 6.3 2.9e-04 -8.146 3.538 AT5G58280|AT5G58280 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -384 -377 CTTCCCGT 5.4 4.2e-04 -7.775 3.377 AT5G58280|AT5G58280 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -297 -290 ATCCACGC 4.8 9.5e-04 -6.959 3.022 AT5G38710|POX2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -124 -117 ACTCCCGT 4.7 9.5e-04 -6.959 3.022 AT1G74370|AT1G74370 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -294 -287 TTCCCCGA 4.8 8.8e-04 -7.036 3.056 AT1G74370|AT1G74370 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -221 -214 GTTTCCGC 5.4 4.2e-04 -7.775 3.377 AT1G74370|AT1G74370 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -43 -36 TATACCGC 5.9 3.1e-04 -8.079 3.509 AT3G04560|AT3G04560 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -377 -370 TTTCCAGC 7.1 1.4e-04 -8.874 3.854 AT1G57140|AT1G57140 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -240 -233 TTTCCCAC 6.9 2.1e-04 -8.468 3.678 AT4G31290|AT4G31290 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -355 -348 TTTCCCAC 6.9 2.1e-04 -8.468 3.678 AT5G06650|GIS2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -205 -198 TTACCCGT 5.3 5.1e-04 -7.581 3.292 AT5G06650|GIS2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -106 -99 ATTCCCGA 6.7 2.5e-04 -8.294 3.602 AT1G17690|NOF1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -489 -482 TTGCCTGC 5.0 8.0e-04 -7.131 3.097 AT1G70890|MLP43 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -361 -354 ATTCCCAC 6.5 2.7e-04 -8.217 3.569 AT4G14550|IAA14 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -347 -340 TTTACCGC 7.6 4.7e-05 -9.965 4.328 AT3G49668|AT3G49668 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -384 -377 TCTGCCGC 5.3 5.1e-04 -7.581 3.292 AT3G49668|AT3G49668 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -327 -320 TTTCCCCC 6.7 2.5e-04 -8.294 3.602 AT3G49668|AT3G49668 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -164 -157 AATCTCGC 4.8 8.8e-04 -7.036 3.056 AT3G49668|AT3G49668 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -158 -151 TTACCGGC 5.3 5.1e-04 -7.581 3.292 AT5G09900|EMB2107 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -317 -310 TTGGCCGC 5.1 7.4e-04 -7.209 3.131 AT5G09900|EMB2107 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -281 -274 TTCCCTGC 4.8 8.8e-04 -7.036 3.056 AT5G09900|EMB2107 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -270 -263 GTTCCCTC 5.2 6.7e-04 -7.308 3.174 AT3G09595|AT3G09595 site 5015_E2Fb_Athamap_20091028_ R -329 -322 TTGTCCGC 5.1 6.5e-04 -7.339 3.187 AT3G09595|AT3G09595 site 5015_E2Fb_Athamap_20091028_ R -180 -173 TTGGCCGC 5.0 6.5e-04 -7.339 3.187 AT3G09595|AT3G09595 site 5015_E2Fb_Athamap_20091028_ D -140 -133 CTTGCCGC 5.4 3.9e-04 -7.849 3.409 AT3G14130|GLO4 site 5015_E2Fb_Athamap_20091028_ D -294 -287 TTCCCCGT 4.8 7.5e-04 -7.195 3.125 AT3G14130|GLO4 site 5015_E2Fb_Athamap_20091028_ R -278 -271 TGTTCCGC 5.1 6.5e-04 -7.339 3.187 AT3G14130|GLO4 site 5015_E2Fb_Athamap_20091028_ R -54 -47 TTGCCCAC 4.7 8.2e-04 -7.106 3.086 AT5G58280|AT5G58280 site 5015_E2Fb_Athamap_20091028_ R -408 -401 CTGCCCGC 6.2 2.8e-04 -8.181 3.553 AT5G58280|AT5G58280 site 5015_E2Fb_Athamap_20091028_ R -384 -377 CTTCCCGT 5.3 5.1e-04 -7.581 3.292 AT1G74370|AT1G74370 site 5015_E2Fb_Athamap_20091028_ R -294 -287 TTCCCCGA 4.8 7.9e-04 -7.143 3.102 AT1G74370|AT1G74370 site 5015_E2Fb_Athamap_20091028_ R -221 -214 GTTTCCGC 5.3 4.4e-04 -7.729 3.357 AT1G74370|AT1G74370 site 5015_E2Fb_Athamap_20091028_ R -43 -36 TATACCGC 5.8 3.1e-04 -8.079 3.509 AT3G04560|AT3G04560 site 5015_E2Fb_Athamap_20091028_ D -377 -370 TTTCCAGC 7.3 1.3e-04 -8.948 3.886 AT1G57140|AT1G57140 site 5015_E2Fb_Athamap_20091028_ R -240 -233 TTTCCCAC 7.1 1.7e-04 -8.680 3.770 AT4G31290|AT4G31290 site 5015_E2Fb_Athamap_20091028_ R -355 -348 TTTCCCAC 7.1 1.7e-04 -8.680 3.770 AT5G06650|GIS2 site 5015_E2Fb_Athamap_20091028_ R -205 -198 TTACCCGT 5.2 5.1e-04 -7.581 3.292 AT5G06650|GIS2 site 5015_E2Fb_Athamap_20091028_ R -106 -99 ATTCCCGA 6.6 2.4e-04 -8.335 3.620 AT1G17690|NOF1 site 5015_E2Fb_Athamap_20091028_ D -489 -482 TTGCCTGC 4.9 6.9e-04 -7.279 3.161 AT1G17690|NOF1 site 5015_E2Fb_Athamap_20091028_ R -49 -42 TTTAACGC 4.5 9.4e-04 -6.970 3.027 AT4G37390|YDK1 site 5015_E2Fb_Athamap_20091028_ D -101 -94 TGTCCCCC 4.5 9.4e-04 -6.970 3.027 AT1G70890|MLP43 site 5015_E2Fb_Athamap_20091028_ D -361 -354 ATTCCCAC 6.3 2.7e-04 -8.217 3.569 AT4G14550|IAA14 site 5015_E2Fb_Athamap_20091028_ D -347 -340 TTTACCGC 7.8 3.7e-05 -10.205 4.432 AT3G49668|AT3G49668 site 5015_E2Fb_Athamap_20091028_ R -384 -377 TCTGCCGC 5.3 5.1e-04 -7.581 3.292 AT3G49668|AT3G49668 site 5015_E2Fb_Athamap_20091028_ D -327 -320 TTTCCCCC 6.9 1.9e-04 -8.568 3.721 AT3G49668|AT3G49668 site 5015_E2Fb_Athamap_20091028_ R -158 -151 TTACCGGC 5.3 5.1e-04 -7.581 3.292 AT5G09900|EMB2107 site 5015_E2Fb_Athamap_20091028_ D -317 -310 TTGGCCGC 5.0 6.5e-04 -7.339 3.187 AT5G09900|EMB2107 site 5015_E2Fb_Athamap_20091028_ D -281 -274 TTCCCTGC 4.7 7.9e-04 -7.143 3.102 AT5G09900|EMB2107 site 5015_E2Fb_Athamap_20091028_ D -270 -263 GTTCCCTC 5.0 6.5e-04 -7.339 3.187 AT3G09595|AT3G09595 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -139 -129 TTGCCGCCCAT 8.8 1.7e-05 -10.982 4.770 AT3G14130|GLO4 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -293 -283 TCCCCGTGATT 4.5 9.8e-04 -6.928 3.009 AT3G01570|AT3G01570 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -338 -328 TTCTCGAGCAA 5.0 6.0e-04 -7.419 3.222 AT3G01570|AT3G01570 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -56 -46 ATCTCGCTCAA 6.9 1.3e-04 -8.948 3.886 AT5G38710|POX2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -123 -113 CTCCCGTCAAA 6.1 2.5e-04 -8.294 3.602 AT1G74370|AT1G74370 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -47 -37 ATACCGCCAAA 7.9 5.3e-05 -9.845 4.276 AT1G57140|AT1G57140 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -244 -234 TTCCCACTCAT 6.9 1.3e-04 -8.948 3.886 AT4G31290|AT4G31290 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -359 -349 TTCCCACGACT 5.2 5.0e-04 -7.601 3.301 AT5G06650|GIS2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -378 -368 TACCCGTCGAA 5.8 3.1e-04 -8.079 3.509 AT5G06650|GIS2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -216 -206 TTCTAGCTATA 4.5 9.1e-04 -7.002 3.041 AT1G17690|NOF1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -488 -478 TGCCTGCCCAA 6.3 2.1e-04 -8.468 3.678 AT4G37390|YDK1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -421 -411 TTGCCTCCAAA 4.8 7.2e-04 -7.236 3.143 AT1G70890|MLP43 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -175 -165 TTCTCACGAAA 4.4 9.8e-04 -6.928 3.009 AT1G28200|FIP1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -405 -395 TAACCGCTATT 6.0 2.9e-04 -8.146 3.538 AT4G29350|PRO2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -176 -166 AACCCGAGAAA 5.3 4.6e-04 -7.684 3.337 AT2G32020|AT2G32020 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -364 -354 TTACAGCGATA 4.8 7.2e-04 -7.236 3.143 AT4G14550|IAA14 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -346 -336 TTACCGCCCAA 9.2 1.0e-05 -11.513 5.000 AT3G49668|AT3G49668 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -326 -316 TTCCCCCAATT 4.4 9.8e-04 -6.928 3.009 AT3G49668|AT3G49668 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -162 -152 TACCGGCGAGA 5.0 6.0e-04 -7.419 3.222 AT5G09900|EMB2107 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -307 -297 GTAGCGCCATT 4.9 6.5e-04 -7.339 3.187 AT5G09900|EMB2107 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -269 -259 TTCCCTCCAAA 8.1 3.9e-05 -10.152 4.409 ; ; 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_ 28 0 ; 2 5015_E2Fb_Athamap_20091028_ 27 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 21 0 ; TOTAL 76 0 ; Host name rsat ; Job started 2026-08-17.170345 ; Job done 2026-08-17.170346 ; Seconds 0.44 ; user 0.44 ; system 0.03 ; cuser 0.8 ; csystem 0.1