; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.165811_GtZZNw.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_2026-08-17.165811_U574zq.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.165811_U574zq.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_2026-08-17.165811_GtZZNw.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 AT1G30010|NMAT1 limit START_END D -500 -1 . 0 0 0 0 AT4G08410|AT4G08410 limit START_END D -500 -1 . 0 0 0 0 AT1G62740|HOP2 limit START_END D -500 -1 . 0 0 0 0 AT5G48020|AT5G48020 limit START_END D -500 -1 . 0 0 0 0 AT1G35183|AT1G35183 limit START_END D -500 -1 . 0 0 0 0 AT5G60280|LECRK18 limit START_END D -500 -1 . 0 0 0 0 AT1G72545|AT1G72545 limit START_END D -500 -1 . 0 0 0 0 AT3G63220|SKIP30 limit START_END D -500 -1 . 0 0 0 0 AT1G80940|AT1G80940 limit START_END D -500 -1 . 0 0 0 0 AT2G16580|AT2G16580 limit START_END D -500 -1 . 0 0 0 0 AT1G26730|PHO1-H7 limit START_END D -500 -1 . 0 0 0 0 AT2G41330|AT2G41330 limit START_END D -500 -1 . 0 0 0 0 AT5G41160|ATPUP12 limit START_END D -500 -1 . 0 0 0 0 AT2G23067|AT2G23067 limit START_END D -500 -1 . 0 0 0 0 AT5G05060|AT5G05060 limit START_END D -500 -1 . 0 0 0 0 AT5G06245|AT5G06245 limit START_END D -500 -1 . 0 0 0 0 AT5G46630|AT5G46630 limit START_END D -500 -1 . 0 0 0 0 AT2G36530|ENO2 limit START_END D -500 -1 . 0 0 0 0 AT3G01205|AT3G01205 limit START_END D -500 -1 . 0 0 0 0 AT4G30872|AT4G30872 limit START_END D -500 -1 . 0 0 0 0 AT1G18580|GAUT11 limit START_END D -500 -1 . 0 0 0 0 AT3G19390|RD21C limit START_END D -500 -1 . 0 0 0 0 AT3G59730|LECRK56 limit START_END D -500 -1 . 0 0 0 0 AT2G37125|AT2G37125 limit START_END D -500 -1 . 0 0 0 0 AT1G30010|NMAT1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -341 -334 TTATCCGC 5.4 4.2e-04 -7.775 3.377 AT1G30010|NMAT1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -199 -192 ATCGCCGC 5.1 6.7e-04 -7.308 3.174 AT1G62740|HOP2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -397 -390 TTTCCAGC 7.1 1.4e-04 -8.874 3.854 AT1G62740|HOP2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -222 -215 TCTCCGGC 5.2 5.9e-04 -7.435 3.229 AT5G48020|AT5G48020 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -318 -311 AGTCCCGC 7.7 3.5e-05 -10.260 4.456 AT5G60280|LECRK18 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -474 -467 ACTCCCGT 4.7 9.5e-04 -6.959 3.022 AT5G60280|LECRK18 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -444 -437 CTTCCCTC 5.2 5.9e-04 -7.435 3.229 AT3G63220|SKIP30 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -436 -429 TTGCCGGC 5.1 7.4e-04 -7.209 3.131 AT1G80940|AT1G80940 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -75 -68 CTTCCGGC 5.5 4.2e-04 -7.775 3.377 AT1G26730|PHO1-H7 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -201 -194 TTCCACGC 5.1 6.7e-04 -7.308 3.174 AT5G41160|ATPUP12 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -467 -460 TTACTCGC 5.6 3.5e-04 -7.958 3.456 AT5G41160|ATPUP12 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -450 -443 CTTCCGGC 5.5 4.2e-04 -7.775 3.377 AT5G41160|ATPUP12 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -438 -431 ATCACCGC 4.8 9.5e-04 -6.959 3.022 AT5G41160|ATPUP12 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -363 -356 TCCCCCGC 5.7 3.4e-04 -7.987 3.469 AT5G41160|ATPUP12 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -289 -282 TCTCCCTC 4.9 8.0e-04 -7.131 3.097 AT5G05060|AT5G05060 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -485 -478 ATTCCCGG 6.6 2.6e-04 -8.255 3.585 AT5G05060|AT5G05060 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -484 -477 TTCCCGGC 4.9 8.0e-04 -7.131 3.097 AT5G46630|AT5G46630 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -143 -136 AATACCGC 5.0 8.0e-04 -7.131 3.097 AT1G18580|GAUT11 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -335 -328 TCTACCGC 5.6 3.5e-04 -7.958 3.456 AT3G19390|RD21C site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -170 -163 TTACACGC 5.5 3.9e-04 -7.849 3.409 AT3G19390|RD21C site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -141 -134 ATTCCCGG 6.6 2.6e-04 -8.255 3.585 AT3G59730|LECRK56 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -468 -461 TTGGCCGC 5.1 7.4e-04 -7.209 3.131 AT3G59730|LECRK56 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -109 -102 TTACCCAC 5.0 7.4e-04 -7.209 3.131 AT2G37125|AT2G37125 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -444 -437 TTACCTGC 5.2 5.9e-04 -7.435 3.229 AT2G37125|AT2G37125 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -155 -148 TTGACCGC 5.1 6.7e-04 -7.308 3.174 AT2G37125|AT2G37125 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -8 -1 TTTCCCCC 6.7 2.5e-04 -8.294 3.602 AT1G30010|NMAT1 site 5015_E2Fb_Athamap_20091028_ R -341 -334 TTATCCGC 5.4 3.9e-04 -7.849 3.409 AT1G30010|NMAT1 site 5015_E2Fb_Athamap_20091028_ D -199 -192 ATCGCCGC 4.7 8.2e-04 -7.106 3.086 AT1G62740|HOP2 site 5015_E2Fb_Athamap_20091028_ R -397 -390 TTTCCAGC 7.3 1.3e-04 -8.948 3.886 AT1G62740|HOP2 site 5015_E2Fb_Athamap_20091028_ R -222 -215 TCTCCGGC 5.1 5.8e-04 -7.452 3.237 AT5G48020|AT5G48020 site 5015_E2Fb_Athamap_20091028_ D -318 -311 AGTCCCGC 7.6 5.8e-05 -9.755 4.237 AT5G60280|LECRK18 site 5015_E2Fb_Athamap_20091028_ D -444 -437 CTTCCCTC 5.0 6.5e-04 -7.339 3.187 AT3G63220|SKIP30 site 5015_E2Fb_Athamap_20091028_ R -436 -429 TTGCCGGC 5.0 6.5e-04 -7.339 3.187 AT3G63220|SKIP30 site 5015_E2Fb_Athamap_20091028_ R -13 -6 TCTCCCCC 4.6 8.2e-04 -7.106 3.086 AT1G80940|AT1G80940 site 5015_E2Fb_Athamap_20091028_ R -75 -68 CTTCCGGC 5.3 4.4e-04 -7.729 3.357 AT1G26730|PHO1-H7 site 5015_E2Fb_Athamap_20091028_ D -201 -194 TTCCACGC 5.1 6.5e-04 -7.339 3.187 AT5G41160|ATPUP12 site 5015_E2Fb_Athamap_20091028_ R -467 -460 TTACTCGC 5.5 3.6e-04 -7.929 3.444 AT5G41160|ATPUP12 site 5015_E2Fb_Athamap_20091028_ R -450 -443 CTTCCGGC 5.3 4.4e-04 -7.729 3.357 AT5G41160|ATPUP12 site 5015_E2Fb_Athamap_20091028_ R -363 -356 TCCCCCGC 5.6 3.3e-04 -8.016 3.481 AT5G41160|ATPUP12 site 5015_E2Fb_Athamap_20091028_ R -361 -354 TCTCCCCC 4.6 8.2e-04 -7.106 3.086 AT5G41160|ATPUP12 site 5015_E2Fb_Athamap_20091028_ R -289 -282 TCTCCCTC 4.8 7.5e-04 -7.195 3.125 AT5G05060|AT5G05060 site 5015_E2Fb_Athamap_20091028_ D -485 -478 ATTCCCGG 6.5 2.5e-04 -8.294 3.602 AT5G05060|AT5G05060 site 5015_E2Fb_Athamap_20091028_ D -484 -477 TTCCCGGC 4.9 7.5e-04 -7.195 3.125 AT5G46630|AT5G46630 site 5015_E2Fb_Athamap_20091028_ D -143 -136 AATACCGC 4.5 9.4e-04 -6.970 3.027 AT1G18580|GAUT11 site 5015_E2Fb_Athamap_20091028_ R -335 -328 TCTACCGC 5.5 3.6e-04 -7.929 3.444 AT3G19390|RD21C site 5015_E2Fb_Athamap_20091028_ R -170 -163 TTACACGC 5.5 3.9e-04 -7.849 3.409 AT3G19390|RD21C site 5015_E2Fb_Athamap_20091028_ R -141 -134 ATTCCCGG 6.5 2.5e-04 -8.294 3.602 AT3G59730|LECRK56 site 5015_E2Fb_Athamap_20091028_ D -468 -461 TTGGCCGC 5.0 6.5e-04 -7.339 3.187 AT3G59730|LECRK56 site 5015_E2Fb_Athamap_20091028_ R -109 -102 TTACCCAC 4.9 6.9e-04 -7.279 3.161 AT2G37125|AT2G37125 site 5015_E2Fb_Athamap_20091028_ D -444 -437 TTACCTGC 5.1 5.8e-04 -7.452 3.237 AT2G37125|AT2G37125 site 5015_E2Fb_Athamap_20091028_ D -155 -148 TTGACCGC 5.1 6.5e-04 -7.339 3.187 AT2G37125|AT2G37125 site 5015_E2Fb_Athamap_20091028_ D -8 -1 TTTCCCCC 6.9 1.9e-04 -8.568 3.721 AT1G30010|NMAT1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -472 -462 TTCACGACATT 4.9 6.5e-04 -7.339 3.187 AT1G30010|NMAT1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -347 -337 TCCGCTCCAAA 4.9 7.2e-04 -7.236 3.143 AT1G30010|NMAT1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -345 -335 TATCCGCTCCA 4.5 9.1e-04 -7.002 3.041 AT1G62740|HOP2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -401 -391 TTCCAGCGATT 7.2 1.0e-04 -9.210 4.000 AT5G48020|AT5G48020 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -317 -307 GTCCCGCCAGT 7.3 9.0e-05 -9.316 4.046 AT5G60280|LECRK18 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -92 -82 TACCTGCAATA 4.7 7.7e-04 -7.169 3.114 AT3G63220|SKIP30 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -25 -15 TACCGGCCTTT 4.8 7.2e-04 -7.236 3.143 AT1G80940|AT1G80940 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -411 -401 TTCTCGTCCTA 5.9 2.9e-04 -8.146 3.538 AT1G80940|AT1G80940 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -386 -376 TGCCCCCCAAA 5.5 3.9e-04 -7.849 3.409 AT1G80940|AT1G80940 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -79 -69 TTCCGGCACAA 6.0 2.7e-04 -8.217 3.569 AT1G26730|PHO1-H7 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -380 -370 AAGCCGCCATA 6.5 1.8e-04 -8.623 3.745 AT2G41330|AT2G41330 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -266 -256 CTCCCACTAAT 4.4 9.8e-04 -6.928 3.009 AT5G41160|ATPUP12 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -454 -444 TTCCGGCGAAT 7.7 6.6e-05 -9.626 4.180 AT5G41160|ATPUP12 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -293 -283 CTCCCTCGCTA 5.8 3.1e-04 -8.079 3.509 AT5G41160|ATPUP12 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -261 -251 AATCCGCCATT 5.8 3.1e-04 -8.079 3.509 AT5G41160|ATPUP12 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -209 -199 TCAGCGCCATT 4.5 9.1e-04 -7.002 3.041 AT5G05060|AT5G05060 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -500 -490 TACGCACCCAA 6.9 1.3e-04 -8.948 3.886 AT5G05060|AT5G05060 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -484 -474 TTCCCGGCTAA 6.6 1.6e-04 -8.740 3.796 AT5G05060|AT5G05060 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -483 -473 TCCCGGCTAAA 4.7 7.7e-04 -7.169 3.114 AT5G46630|AT5G46630 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -321 -311 TACCCTCTCTT 5.8 3.1e-04 -8.079 3.509 AT5G46630|AT5G46630 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -131 -121 CACCTGCGCTA 4.7 7.7e-04 -7.169 3.114 AT5G46630|AT5G46630 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -12 -2 TACAGGCCCAT 4.5 9.1e-04 -7.002 3.041 AT4G30872|AT4G30872 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -493 -483 AGCCCACCAAT 4.5 9.1e-04 -7.002 3.041 AT1G18580|GAUT11 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -339 -329 CTACCGCCAAA 6.5 1.9e-04 -8.568 3.721 AT3G19390|RD21C site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -174 -164 TACACGCACTT 5.1 6.0e-04 -7.419 3.222 AT2G37125|AT2G37125 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -443 -433 TACCTGCAATA 4.7 7.7e-04 -7.169 3.114 AT2G37125|AT2G37125 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -152 -142 ACCGCGCCATT 7.1 1.2e-04 -9.028 3.921 ; ; 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_ 26 0 ; 2 5015_E2Fb_Athamap_20091028_ 26 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 27 0 ; TOTAL 79 0 ; Host name rsat ; Job started 2026-08-17.165812 ; Job done 2026-08-17.165813 ; Seconds 0.47 ; user 0.47 ; system 0.04 ; cuser 0.72 ; csystem 0.1