; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.110423_kgBkFQ.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_2026-08-17.110423_2G9K8T.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_2026-08-17.110423_2G9K8T.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.110423_kgBkFQ.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 AT3G52240|AT3G52240 limit START_END D -500 -1 . 0 0 0 0 AT2G31530|SCY2 limit START_END D -500 -1 . 0 0 0 0 AT5G67400|PER73 limit START_END D -500 -1 . 0 0 0 0 AT1G68880|BZIP8 limit START_END D -500 -1 . 0 0 0 0 AT2G28770|AT2G28770 limit START_END D -500 -1 . 0 0 0 0 AT1G29110|AT1G29110 limit START_END D -500 -1 . 0 0 0 0 AT3G10730|SUN2 limit START_END D -500 -1 . 0 0 0 0 AT4G16892|AT4G16892 limit START_END D -500 -1 . 0 0 0 0 AT2G42475|AT2G42475 limit START_END D -500 -1 . 0 0 0 0 AT5G17167|AT5G17167 limit START_END D -500 -1 . 0 0 0 0 AT5G02410|ALG10 limit START_END D -500 -1 . 0 0 0 0 AT4G10560|MEE53 limit START_END D -500 -1 . 0 0 0 0 ATMG00230|TRNS.1 limit START_END D -500 -1 . 0 0 0 0 AT1G47056|VFB1 limit START_END D -500 -1 . 0 0 0 0 AT1G78560|BASS1 limit START_END D -500 -1 . 0 0 0 0 AT1G09323|AT1G09323 limit START_END D -500 -1 . 0 0 0 0 AT5G20854|ATC2 limit START_END D -500 -1 . 0 0 0 0 AT5G45400|RPA1C limit START_END D -500 -1 . 0 0 0 0 AT3G43660|AT3G43660 limit START_END D -500 -1 . 0 0 0 0 AT2G23140|AT2G23140 limit START_END D -500 -1 . 0 0 0 0 AT1G66360|CAR2 limit START_END D -500 -1 . 0 0 0 0 AT5G44220|AT5G44220 limit START_END D -500 -1 . 0 0 0 0 AT1G27900|AT1G27900 limit START_END D -500 -1 . 0 0 0 0 AT3G52240|AT3G52240 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -455 -448 GTTTCCGC 5.4 4.2e-04 -7.775 3.377 AT3G52240|AT3G52240 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -373 -366 TTCACCGC 5.1 6.7e-04 -7.308 3.174 AT2G31530|SCY2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -304 -297 TCTCCTGC 5.1 6.7e-04 -7.308 3.174 AT1G68880|BZIP8 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -419 -412 ACTCTCGC 5.0 8.0e-04 -7.131 3.097 AT1G68880|BZIP8 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -305 -298 TTACCCAC 5.0 7.4e-04 -7.209 3.131 AT1G68880|BZIP8 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -177 -170 TCTCACGC 5.4 4.2e-04 -7.775 3.377 AT1G68880|BZIP8 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -135 -128 TTCTCCGC 5.2 5.9e-04 -7.435 3.229 AT2G28770|AT2G28770 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -433 -426 ACTCCCGT 4.7 9.5e-04 -6.959 3.022 AT2G28770|AT2G28770 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -385 -378 TTTAGCGC 4.8 8.8e-04 -7.036 3.056 AT2G28770|AT2G28770 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -237 -230 AATCTCGC 4.8 8.8e-04 -7.036 3.056 AT3G10730|SUN2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -434 -427 TCTCCCGC 8.2 1.9e-05 -10.871 4.721 AT3G10730|SUN2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -101 -94 TTTCACGC 7.4 6.6e-05 -9.626 4.180 AT4G16892|AT4G16892 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -384 -377 CTTCCCAC 5.1 6.7e-04 -7.308 3.174 AT4G16892|AT4G16892 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -364 -357 TCTCGCGC 5.7 3.4e-04 -7.987 3.469 AT4G16892|AT4G16892 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -362 -355 TCTCTCGC 5.4 4.2e-04 -7.775 3.377 AT4G16892|AT4G16892 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -348 -341 ATTCCGGC 6.8 2.1e-04 -8.468 3.678 AT4G16892|AT4G16892 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -8 -1 TCTCGCGC 5.7 3.4e-04 -7.987 3.469 AT2G42475|AT2G42475 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -346 -339 TTTCCCGG 7.0 1.6e-04 -8.740 3.796 AT5G17167|AT5G17167 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -353 -346 TATCCAGC 5.3 5.1e-04 -7.581 3.292 ATMG00230|TRNS.1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -445 -438 ACCCCCGC 5.2 5.9e-04 -7.435 3.229 ATMG00230|TRNS.1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -373 -366 TTTACCGC 7.6 4.7e-05 -9.965 4.328 AT1G47056|VFB1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -379 -372 TTTACCGC 7.6 4.7e-05 -9.965 4.328 AT1G47056|VFB1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -317 -310 TATCTCGC 5.7 3.4e-04 -7.987 3.469 AT5G45400|RPA1C site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -22 -15 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 AT3G43660|AT3G43660 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -491 -484 AAGCCCGC 5.4 4.2e-04 -7.775 3.377 AT3G52240|AT3G52240 site 5015_E2Fb_Athamap_20091028_ R -455 -448 GTTTCCGC 5.3 4.4e-04 -7.729 3.357 AT3G52240|AT3G52240 site 5015_E2Fb_Athamap_20091028_ D -373 -366 TTCACCGC 5.1 6.5e-04 -7.339 3.187 AT3G52240|AT3G52240 site 5015_E2Fb_Athamap_20091028_ D -130 -123 TTTCGCGT 4.6 8.2e-04 -7.106 3.086 AT2G31530|SCY2 site 5015_E2Fb_Athamap_20091028_ D -304 -297 TCTCCTGC 5.0 6.5e-04 -7.339 3.187 AT1G68880|BZIP8 site 5015_E2Fb_Athamap_20091028_ D -419 -412 ACTCTCGC 4.5 9.4e-04 -6.970 3.027 AT1G68880|BZIP8 site 5015_E2Fb_Athamap_20091028_ D -305 -298 TTACCCAC 4.9 6.9e-04 -7.279 3.161 AT1G68880|BZIP8 site 5015_E2Fb_Athamap_20091028_ D -177 -170 TCTCACGC 5.3 4.4e-04 -7.729 3.357 AT1G68880|BZIP8 site 5015_E2Fb_Athamap_20091028_ D -135 -128 TTCTCCGC 5.1 5.8e-04 -7.452 3.237 AT2G28770|AT2G28770 site 5015_E2Fb_Athamap_20091028_ R -385 -378 TTTAGCGC 4.7 7.9e-04 -7.143 3.102 AT3G10730|SUN2 site 5015_E2Fb_Athamap_20091028_ D -434 -427 TCTCCCGC 8.4 2.1e-05 -10.771 4.678 AT3G10730|SUN2 site 5015_E2Fb_Athamap_20091028_ R -101 -94 TTTCACGC 7.6 5.8e-05 -9.755 4.237 AT4G16892|AT4G16892 site 5015_E2Fb_Athamap_20091028_ R -384 -377 CTTCCCAC 5.0 6.9e-04 -7.279 3.161 AT4G16892|AT4G16892 site 5015_E2Fb_Athamap_20091028_ R -364 -357 TCTCGCGC 5.6 3.3e-04 -8.016 3.481 AT4G16892|AT4G16892 site 5015_E2Fb_Athamap_20091028_ R -362 -355 TCTCTCGC 5.4 4.4e-04 -7.729 3.357 AT4G16892|AT4G16892 site 5015_E2Fb_Athamap_20091028_ R -348 -341 ATTCCGGC 6.7 2.1e-04 -8.468 3.678 AT4G16892|AT4G16892 site 5015_E2Fb_Athamap_20091028_ R -8 -1 TCTCGCGC 5.6 3.3e-04 -8.016 3.481 AT2G42475|AT2G42475 site 5015_E2Fb_Athamap_20091028_ R -346 -339 TTTCCCGG 7.2 1.4e-04 -8.874 3.854 AT5G17167|AT5G17167 site 5015_E2Fb_Athamap_20091028_ R -353 -346 TATCCAGC 5.3 4.4e-04 -7.729 3.357 ATMG00230|TRNS.1 site 5015_E2Fb_Athamap_20091028_ D -445 -438 ACCCCCGC 4.8 7.5e-04 -7.195 3.125 ATMG00230|TRNS.1 site 5015_E2Fb_Athamap_20091028_ R -373 -366 TTTACCGC 7.8 3.7e-05 -10.205 4.432 AT1G47056|VFB1 site 5015_E2Fb_Athamap_20091028_ R -379 -372 TTTACCGC 7.8 3.7e-05 -10.205 4.432 AT1G47056|VFB1 site 5015_E2Fb_Athamap_20091028_ R -317 -310 TATCTCGC 5.6 3.3e-04 -8.016 3.481 AT5G45400|RPA1C site 5015_E2Fb_Athamap_20091028_ D -22 -15 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 AT3G43660|AT3G43660 site 5015_E2Fb_Athamap_20091028_ R -491 -484 AAGCCCGC 5.0 6.5e-04 -7.339 3.187 AT3G52240|AT3G52240 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -459 -449 TTTCCGCTCTT 6.8 1.4e-04 -8.874 3.854 AT5G67400|PER73 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -244 -234 TTCAGGCCCAT 5.3 5.0e-04 -7.601 3.301 AT2G28770|AT2G28770 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -437 -427 CTCCCGTCAAT 6.0 2.7e-04 -8.217 3.569 AT2G28770|AT2G28770 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -389 -379 TTAGCGCAATA 4.9 6.5e-04 -7.339 3.187 AT2G28770|AT2G28770 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -388 -378 ATTGCGCTAAA 5.1 5.4e-04 -7.524 3.268 AT2G28770|AT2G28770 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -372 -362 ATCGCACCATT 5.9 2.9e-04 -8.146 3.538 AT2G28770|AT2G28770 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -342 -332 TTCTCGACAAA 5.4 4.2e-04 -7.775 3.377 AT1G29110|AT1G29110 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -67 -57 TTCTCCCCATT 4.4 9.8e-04 -6.928 3.009 AT3G10730|SUN2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -433 -423 CTCCCGCCACA 7.5 7.5e-05 -9.498 4.125 AT4G16892|AT4G16892 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -388 -378 TTCCCACTATC 4.6 8.3e-04 -7.094 3.081 AT4G16892|AT4G16892 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -368 -358 CTCGCGCCTAA 7.0 1.2e-04 -9.028 3.921 AT5G17167|AT5G17167 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -47 -37 ATCAAGCCCAA 4.4 9.8e-04 -6.928 3.009 ATMG00230|TRNS.1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -377 -367 TTACCGCCCGC 5.1 5.4e-04 -7.524 3.268 ATMG00230|TRNS.1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -207 -197 ATCCCGTTATA 6.2 2.3e-04 -8.377 3.638 AT5G45400|RPA1C site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -21 -11 TTCCCTCTAAA 7.0 1.3e-04 -8.948 3.886 AT3G43660|AT3G43660 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -495 -485 AGCCCGCCTAT 6.6 1.8e-04 -8.623 3.745 AT1G66360|CAR2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -274 -264 AAGCCGCGATT 5.2 5.0e-04 -7.601 3.301 ; ; 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 23 ; Sum of sequence lengths 11500 ; N residues 0 ; Matches per matrix ; matrix name matches scored ; 1 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ 25 0 ; 2 5015_E2Fb_Athamap_20091028_ 24 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 17 0 ; TOTAL 66 0 ; Host name rsat ; Job started 2026-08-17.110424 ; Job done 2026-08-17.110425 ; Seconds 0.47 ; user 0.47 ; system 0.03 ; cuser 0.78 ; csystem 0.11