; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.110751_PVk2ma.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_2026-08-17.110751_RVIl73.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.110751_RVIl73.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_2026-08-17.110751_PVk2ma.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 AT5G26670|PAE10 limit START_END D -500 -1 . 0 0 0 0 AT5G07725|AT5G07725 limit START_END D -500 -1 . 0 0 0 0 AT3G20620|AT3G20620 limit START_END D -500 -1 . 0 0 0 0 AT3G53235|AT3G53235 limit START_END D -500 -1 . 0 0 0 0 AT5G12390|FIS1B limit START_END D -500 -1 . 0 0 0 0 AT5G62180|CXE20 limit START_END D -500 -1 . 0 0 0 0 AT3G11270|RPN8B limit START_END D -500 -1 . 0 0 0 0 AT2G18660|EGC2 limit START_END D -500 -1 . 0 0 0 0 AT1G72460|AT1G72460 limit START_END D -500 -1 . 0 0 0 0 AT1G17730|CHMP1A limit START_END D -500 -1 . 0 0 0 0 AT1G20440|COR47 limit START_END D -500 -1 . 0 0 0 0 AT5G66690|UGT72E2 limit START_END D -500 -1 . 0 0 0 0 AT2G27000|CYP705A8 limit START_END D -500 -1 . 0 0 0 0 AT3G26135|AT3G26135 limit START_END D -500 -1 . 0 0 0 0 ATCG00820|RPS19 limit START_END D -500 -1 . 0 0 0 0 AT5G43745|AT5G43745 limit START_END D -500 -1 . 0 0 0 0 AT4G05155|AT4G05155 limit START_END D -500 -1 . 0 0 0 0 AT3G07345|AT3G07345 limit START_END D -500 -1 . 0 0 0 0 AT3G58010|PAP9 limit START_END D -500 -1 . 0 0 0 0 AT3G14040|AT3G14040 limit START_END D -500 -1 . 0 0 0 0 AT1G72210|BHLH96 limit START_END D -500 -1 . 0 0 0 0 ATMG01140|ORF152B limit START_END D -500 -1 . 0 0 0 0 AT2G07715|AT2G07715 limit START_END D -500 -1 . 0 0 0 0 AT5G26670|PAE10 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -11 -4 AATCACGC 4.8 9.5e-04 -6.959 3.022 AT5G07725|AT5G07725 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -469 -462 AGTCCCGT 4.7 9.5e-04 -6.959 3.022 AT5G07725|AT5G07725 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -460 -453 TCTCCGGC 5.2 5.9e-04 -7.435 3.229 AT5G07725|AT5G07725 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -393 -386 TTGCCCGT 5.0 7.4e-04 -7.209 3.131 AT5G07725|AT5G07725 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -10 -3 TCTCCCTC 4.9 8.0e-04 -7.131 3.097 AT3G53235|AT3G53235 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -339 -332 TTGCCCGA 5.0 8.0e-04 -7.131 3.097 AT3G53235|AT3G53235 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -10 -3 TTACCAGC 5.2 5.9e-04 -7.435 3.229 AT5G12390|FIS1B site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -331 -324 CTTCCAGC 5.3 5.1e-04 -7.581 3.292 AT5G12390|FIS1B site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -299 -292 ATTCCGGC 6.8 2.1e-04 -8.468 3.678 AT5G12390|FIS1B site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -254 -247 CTTCCGGC 5.5 4.2e-04 -7.775 3.377 AT5G62180|CXE20 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -395 -388 TCTTCCGC 5.2 5.9e-04 -7.435 3.229 AT2G18660|EGC2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -300 -293 TTTCCCGA 7.1 1.4e-04 -8.874 3.854 AT2G18660|EGC2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -230 -223 ATACCCTC 4.7 9.5e-04 -6.959 3.022 AT1G72460|AT1G72460 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -50 -43 ATTCGCGC 7.4 7.6e-05 -9.485 4.119 AT1G17730|CHMP1A site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -396 -389 TTTCCCCC 6.7 2.5e-04 -8.294 3.602 AT1G17730|CHMP1A site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -223 -216 TCTACCGC 5.6 3.5e-04 -7.958 3.456 AT5G66690|UGT72E2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -346 -339 TTAACCGC 5.3 5.1e-04 -7.581 3.292 AT2G27000|CYP705A8 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -376 -369 TTTCCAGC 7.1 1.4e-04 -8.874 3.854 ATCG00820|RPS19 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -302 -295 TTTCCCAC 6.9 2.1e-04 -8.468 3.678 ATCG00820|RPS19 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -131 -124 TATCCTGC 5.3 5.1e-04 -7.581 3.292 AT4G05155|AT4G05155 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -130 -123 TATCCGGC 5.5 4.2e-04 -7.775 3.377 AT3G58010|PAP9 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -491 -484 TTACACGC 5.5 3.9e-04 -7.849 3.409 AT3G58010|PAP9 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -213 -206 ATGACCGC 4.8 9.5e-04 -6.959 3.022 AT1G72210|BHLH96 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -274 -267 ATGACCGC 4.8 9.5e-04 -6.959 3.022 AT1G72210|BHLH96 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -252 -245 TTCCCCGA 4.8 8.8e-04 -7.036 3.056 AT1G72210|BHLH96 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -55 -48 ATCACCGC 4.8 9.5e-04 -6.959 3.022 ATMG01140|ORF152B site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -23 -16 TTACCTGC 5.2 5.9e-04 -7.435 3.229 AT2G07715|AT2G07715 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -463 -456 ATTTCCGC 6.8 2.1e-04 -8.468 3.678 AT2G07715|AT2G07715 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -284 -277 CTTTCCGC 5.4 4.2e-04 -7.775 3.377 AT2G07715|AT2G07715 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -228 -221 GTTCCCCC 4.9 8.0e-04 -7.131 3.097 AT2G07715|AT2G07715 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -99 -92 CTTCCCGA 5.3 5.1e-04 -7.581 3.292 AT5G07725|AT5G07725 site 5015_E2Fb_Athamap_20091028_ R -460 -453 TCTCCGGC 5.1 5.8e-04 -7.452 3.237 AT5G07725|AT5G07725 site 5015_E2Fb_Athamap_20091028_ D -393 -386 TTGCCCGT 5.0 6.9e-04 -7.279 3.161 AT5G07725|AT5G07725 site 5015_E2Fb_Athamap_20091028_ R -10 -3 TCTCCCTC 4.8 7.5e-04 -7.195 3.125 AT3G53235|AT3G53235 site 5015_E2Fb_Athamap_20091028_ R -339 -332 TTGCCCGA 4.9 6.9e-04 -7.279 3.161 AT3G53235|AT3G53235 site 5015_E2Fb_Athamap_20091028_ R -10 -3 TTACCAGC 5.1 5.8e-04 -7.452 3.237 AT5G12390|FIS1B site 5015_E2Fb_Athamap_20091028_ D -331 -324 CTTCCAGC 5.2 5.1e-04 -7.581 3.292 AT5G12390|FIS1B site 5015_E2Fb_Athamap_20091028_ D -299 -292 ATTCCGGC 6.7 2.1e-04 -8.468 3.678 AT5G12390|FIS1B site 5015_E2Fb_Athamap_20091028_ D -254 -247 CTTCCGGC 5.3 4.4e-04 -7.729 3.357 AT5G62180|CXE20 site 5015_E2Fb_Athamap_20091028_ D -395 -388 TCTTCCGC 5.1 5.8e-04 -7.452 3.237 AT2G18660|EGC2 site 5015_E2Fb_Athamap_20091028_ D -300 -293 TTTCCCGA 7.3 1.3e-04 -8.948 3.886 AT1G72460|AT1G72460 site 5015_E2Fb_Athamap_20091028_ D -50 -43 ATTCGCGC 7.2 1.4e-04 -8.874 3.854 AT1G17730|CHMP1A site 5015_E2Fb_Athamap_20091028_ R -396 -389 TTTCCCCC 6.9 1.9e-04 -8.568 3.721 AT1G17730|CHMP1A site 5015_E2Fb_Athamap_20091028_ R -223 -216 TCTACCGC 5.5 3.6e-04 -7.929 3.444 AT5G66690|UGT72E2 site 5015_E2Fb_Athamap_20091028_ R -346 -339 TTAACCGC 5.3 5.1e-04 -7.581 3.292 AT2G27000|CYP705A8 site 5015_E2Fb_Athamap_20091028_ D -376 -369 TTTCCAGC 7.3 1.3e-04 -8.948 3.886 ATCG00820|RPS19 site 5015_E2Fb_Athamap_20091028_ R -383 -376 TTCCCCTC 4.6 8.2e-04 -7.106 3.086 ATCG00820|RPS19 site 5015_E2Fb_Athamap_20091028_ R -302 -295 TTTCCCAC 7.1 1.7e-04 -8.680 3.770 ATCG00820|RPS19 site 5015_E2Fb_Athamap_20091028_ D -131 -124 TATCCTGC 5.3 5.1e-04 -7.581 3.292 AT4G05155|AT4G05155 site 5015_E2Fb_Athamap_20091028_ D -130 -123 TATCCGGC 5.4 3.9e-04 -7.849 3.409 AT3G58010|PAP9 site 5015_E2Fb_Athamap_20091028_ D -491 -484 TTACACGC 5.5 3.9e-04 -7.849 3.409 AT1G72210|BHLH96 site 5015_E2Fb_Athamap_20091028_ R -252 -245 TTCCCCGA 4.8 7.9e-04 -7.143 3.102 ATMG01140|ORF152B site 5015_E2Fb_Athamap_20091028_ R -23 -16 TTACCTGC 5.1 5.8e-04 -7.452 3.237 AT2G07715|AT2G07715 site 5015_E2Fb_Athamap_20091028_ R -463 -456 ATTTCCGC 6.7 2.1e-04 -8.468 3.678 AT2G07715|AT2G07715 site 5015_E2Fb_Athamap_20091028_ R -284 -277 CTTTCCGC 5.3 4.4e-04 -7.729 3.357 AT2G07715|AT2G07715 site 5015_E2Fb_Athamap_20091028_ R -228 -221 GTTCCCCC 4.8 7.9e-04 -7.143 3.102 AT2G07715|AT2G07715 site 5015_E2Fb_Athamap_20091028_ R -99 -92 CTTCCCGA 5.2 5.1e-04 -7.581 3.292 AT5G26670|PAE10 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -326 -316 ATCCTGCACAA 4.9 6.5e-04 -7.339 3.187 AT5G26670|PAE10 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -133 -123 TTATCGCTCAT 4.5 9.1e-04 -7.002 3.041 AT5G07725|AT5G07725 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -146 -136 CTCCGGCGATT 5.0 6.5e-04 -7.339 3.187 AT5G12390|FIS1B site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -330 -320 TTCCAGCCATA 8.5 2.4e-05 -10.637 4.620 AT5G12390|FIS1B site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -298 -288 TTCCGGCCACT 6.2 2.5e-04 -8.294 3.602 AT2G18660|EGC2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -229 -219 TACCCTCCTTA 5.2 5.0e-04 -7.601 3.301 AT1G72460|AT1G72460 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -50 -40 ATGGCGCGAAT 5.6 3.6e-04 -7.929 3.444 AT1G72460|AT1G72460 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -49 -39 TTCGCGCCATA 11.3 1.1e-06 -13.720 5.959 AT2G27000|CYP705A8 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -375 -365 TTCCAGCCATT 7.8 5.3e-05 -9.845 4.276 AT3G26135|AT3G26135 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -290 -280 TATCAGCCCAT 4.4 9.8e-04 -6.928 3.009 ATCG00820|RPS19 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -267 -257 ATCCGGCTCTA 6.5 1.8e-04 -8.623 3.745 ATCG00820|RPS19 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -178 -168 AGCCCTCCCTT 4.5 9.1e-04 -7.002 3.041 AT4G05155|AT4G05155 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -129 -119 ATCCGGCGAAA 6.8 1.4e-04 -8.874 3.854 AT3G07345|AT3G07345 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -360 -350 ACCACGCCCTT 5.0 6.0e-04 -7.419 3.222 AT3G07345|AT3G07345 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -187 -177 AACCTGCCAAA 6.0 2.7e-04 -8.217 3.569 AT3G58010|PAP9 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -490 -480 TACACGCAAAA 5.0 6.0e-04 -7.419 3.222 AT1G72210|BHLH96 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -139 -129 TTCCTGTCCAT 5.1 5.4e-04 -7.524 3.268 AT2G07715|AT2G07715 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -467 -457 TTTCCGCCTAT 6.5 1.8e-04 -8.623 3.745 AT2G07715|AT2G07715 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -321 -311 TTCGGGCACTA 4.8 7.2e-04 -7.236 3.143 AT2G07715|AT2G07715 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -288 -278 TTTCCGCTCAT 7.2 1.0e-04 -9.210 4.000 ; ; 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_ 31 0 ; 2 5015_E2Fb_Athamap_20091028_ 26 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 20 0 ; TOTAL 77 0 ; Host name rsat ; Job started 2026-08-17.110751 ; Job done 2026-08-17.110753 ; Seconds 0.49 ; user 0.49 ; system 0.04 ; cuser 0.8 ; csystem 0.08