; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.132640_5COPHd.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_2026-08-17.132640_08f3ca.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.132640_08f3ca.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_2026-08-17.132640_5COPHd.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 AT3G50050 limit START_END D -500 -1 . 0 0 0 0 SUM2 limit START_END D -500 -1 . 0 0 0 0 ARI5 limit START_END D -500 -1 . 0 0 0 0 AL5 limit START_END D -500 -1 . 0 0 0 0 OBAP1B limit START_END D -500 -1 . 0 0 0 0 RPI3 limit START_END D -500 -1 . 0 0 0 0 AT2G08305 limit START_END D -500 -1 . 0 0 0 0 AT5G52545 limit START_END D -500 -1 . 0 0 0 0 AT5G38005 limit START_END D -500 -1 . 0 0 0 0 UXS3 limit START_END D -500 -1 . 0 0 0 0 AT3G14595 limit START_END D -500 -1 . 0 0 0 0 AT5G08565 limit START_END D -500 -1 . 0 0 0 0 AT2G09575 limit START_END D -500 -1 . 0 0 0 0 AT1G14680 limit START_END D -500 -1 . 0 0 0 0 AT3G10200 limit START_END D -500 -1 . 0 0 0 0 MIR166A limit START_END D -500 -1 . 0 0 0 0 EDR1 limit START_END D -500 -1 . 0 0 0 0 TOPP5 limit START_END D -500 -1 . 0 0 0 0 AT5G22850 limit START_END D -500 -1 . 0 0 0 0 AT4G39790 limit START_END D -500 -1 . 0 0 0 0 AT2G20620 limit START_END D -500 -1 . 0 0 0 0 AT5G00880 limit START_END D -500 -1 . 0 0 0 0 AT4G20830 limit START_END D -500 -1 . 0 0 0 0 AT3G51895 limit START_END D -500 -1 . 0 0 0 0 AL5 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -99 -92 TTTCCCGA 7.1 1.4e-04 -8.874 3.854 OBAP1B site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -383 -376 TCTCCCTC 4.9 8.0e-04 -7.131 3.097 OBAP1B site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -362 -355 TCTCCCTC 4.9 8.0e-04 -7.131 3.097 RPI3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -391 -384 CTTCCCAC 5.1 6.7e-04 -7.308 3.174 RPI3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -291 -284 ATGTCCGC 4.8 9.5e-04 -6.959 3.022 AT2G08305 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -338 -331 TTGCCTGC 5.0 8.0e-04 -7.131 3.097 AT2G08305 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -142 -135 TGTCCCAC 4.8 8.8e-04 -7.036 3.056 AT2G08305 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -14 -7 TTACCAGC 5.2 5.9e-04 -7.435 3.229 AT5G38005 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -31 -24 TTTCCCGT 7.2 1.4e-04 -8.874 3.854 UXS3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -48 -41 ATTTCCGC 6.8 2.1e-04 -8.468 3.678 AT3G14595 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -326 -319 TATCCCAC 5.1 6.7e-04 -7.308 3.174 AT2G09575 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -320 -313 CTTCCCGC 8.5 1.5e-05 -11.107 4.824 AT2G09575 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -261 -254 TTACACGC 5.5 3.9e-04 -7.849 3.409 AT2G09575 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -68 -61 TTTCCCCC 6.7 2.5e-04 -8.294 3.602 AT1G14680 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -382 -375 ACTCTCGC 5.0 8.0e-04 -7.131 3.097 EDR1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -198 -191 TCTCCCGC 8.2 1.9e-05 -10.871 4.721 EDR1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -133 -126 TTACCCGA 5.2 5.9e-04 -7.435 3.229 EDR1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -91 -84 TTAGCCGC 5.5 3.9e-04 -7.849 3.409 AT4G39790 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -377 -370 ATTCCTGC 6.7 2.5e-04 -8.294 3.602 AT4G39790 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -344 -337 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 AT5G00880 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -401 -394 TTTCCCAC 6.9 2.1e-04 -8.468 3.678 AT5G00880 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -283 -276 TTACCTGC 5.2 5.9e-04 -7.435 3.229 AT5G00880 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -224 -217 TTACCGGC 5.3 5.1e-04 -7.581 3.292 AT4G20830 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -36 -29 ATAACCGC 5.0 8.0e-04 -7.131 3.097 AT3G51895 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -248 -241 TGTCCCGA 5.0 7.4e-04 -7.209 3.131 AL5 site 5015_E2Fb_Athamap_20091028_ D -99 -92 TTTCCCGA 7.3 1.3e-04 -8.948 3.886 OBAP1B site 5015_E2Fb_Athamap_20091028_ R -383 -376 TCTCCCTC 4.8 7.5e-04 -7.195 3.125 OBAP1B site 5015_E2Fb_Athamap_20091028_ R -362 -355 TCTCCCTC 4.8 7.5e-04 -7.195 3.125 RPI3 site 5015_E2Fb_Athamap_20091028_ D -391 -384 CTTCCCAC 5.0 6.9e-04 -7.279 3.161 AT2G08305 site 5015_E2Fb_Athamap_20091028_ D -338 -331 TTGCCTGC 4.9 6.9e-04 -7.279 3.161 AT2G08305 site 5015_E2Fb_Athamap_20091028_ R -142 -135 TGTCCCAC 4.7 7.9e-04 -7.143 3.102 AT2G08305 site 5015_E2Fb_Athamap_20091028_ R -14 -7 TTACCAGC 5.1 5.8e-04 -7.452 3.237 AT5G38005 site 5015_E2Fb_Athamap_20091028_ D -31 -24 TTTCCCGT 7.4 1.3e-04 -8.948 3.886 UXS3 site 5015_E2Fb_Athamap_20091028_ D -48 -41 ATTTCCGC 6.7 2.1e-04 -8.468 3.678 AT3G14595 site 5015_E2Fb_Athamap_20091028_ R -326 -319 TATCCCAC 5.1 6.5e-04 -7.339 3.187 AT2G09575 site 5015_E2Fb_Athamap_20091028_ D -320 -313 CTTCCCGC 8.6 1.5e-05 -11.107 4.824 AT2G09575 site 5015_E2Fb_Athamap_20091028_ D -261 -254 TTACACGC 5.5 3.9e-04 -7.849 3.409 AT2G09575 site 5015_E2Fb_Athamap_20091028_ R -68 -61 TTTCCCCC 6.9 1.9e-04 -8.568 3.721 AT1G14680 site 5015_E2Fb_Athamap_20091028_ R -382 -375 ACTCTCGC 4.5 9.4e-04 -6.970 3.027 EDR1 site 5015_E2Fb_Athamap_20091028_ D -198 -191 TCTCCCGC 8.4 2.1e-05 -10.771 4.678 EDR1 site 5015_E2Fb_Athamap_20091028_ R -133 -126 TTACCCGA 5.2 5.8e-04 -7.452 3.237 EDR1 site 5015_E2Fb_Athamap_20091028_ D -91 -84 TTAGCCGC 5.5 3.9e-04 -7.849 3.409 AT4G39790 site 5015_E2Fb_Athamap_20091028_ R -377 -370 ATTCCTGC 6.6 2.5e-04 -8.294 3.602 AT4G39790 site 5015_E2Fb_Athamap_20091028_ D -344 -337 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 AT5G00880 site 5015_E2Fb_Athamap_20091028_ R -401 -394 TTTCCCAC 7.1 1.7e-04 -8.680 3.770 AT5G00880 site 5015_E2Fb_Athamap_20091028_ R -283 -276 TTACCTGC 5.1 5.8e-04 -7.452 3.237 AT5G00880 site 5015_E2Fb_Athamap_20091028_ D -224 -217 TTACCGGC 5.3 5.1e-04 -7.581 3.292 AT4G20830 site 5015_E2Fb_Athamap_20091028_ R -36 -29 ATAACCGC 4.5 9.4e-04 -6.970 3.027 AT3G51895 site 5015_E2Fb_Athamap_20091028_ R -248 -241 TGTCCCGA 5.0 6.9e-04 -7.279 3.161 SUM2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -454 -444 TAACCGACCAT 4.4 9.8e-04 -6.928 3.009 SUM2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -127 -117 AACCAGCCCAT 6.3 2.3e-04 -8.377 3.638 AL5 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -379 -369 TTCCTGTCCAA 5.2 5.0e-04 -7.601 3.301 AL5 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -98 -88 TTCCCGACAAA 8.5 2.4e-05 -10.637 4.620 RPI3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -390 -380 TTCCCACCCAA 8.5 2.7e-05 -10.520 4.569 RPI3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -122 -112 AACCTGCTAAA 4.8 7.2e-04 -7.236 3.143 AT2G08305 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -18 -8 TACCAGCTAAA 6.4 2.1e-04 -8.468 3.678 AT5G52545 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -41 -31 TTACAGCCATA 5.4 4.2e-04 -7.775 3.377 AT5G38005 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -126 -116 TTCGCACCTTA 5.2 5.0e-04 -7.601 3.301 AT5G38005 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -30 -20 TTCCCGTGTTT 4.6 8.3e-04 -7.094 3.081 AT5G08565 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -497 -487 TTCCGGTCAAT 4.8 7.2e-04 -7.236 3.143 AT5G08565 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -129 -119 TTCAGGCCCTT 4.8 7.2e-04 -7.236 3.143 AT2G09575 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -452 -442 TTCGCACTCTA 6.4 1.9e-04 -8.568 3.721 AT2G09575 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -319 -309 TTCCCGCTAAG 8.6 2.1e-05 -10.771 4.678 AT2G09575 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -71 -61 TTTCCCCCATA 4.6 8.3e-04 -7.094 3.081 AT1G14680 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -386 -376 CTCTCGCTAAA 5.3 4.6e-04 -7.684 3.337 EDR1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -197 -187 CTCCCGCTCGA 6.6 1.6e-04 -8.740 3.796 EDR1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -91 -81 TACGCGGCTAA 5.1 5.4e-04 -7.524 3.268 AT4G39790 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -343 -333 TTCCCTCCCTC 6.1 2.5e-04 -8.294 3.602 AT2G20620 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -20 -10 TTCGCACCAAA 7.3 9.0e-05 -9.316 4.046 ; ; 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_ 25 0 ; 2 5015_E2Fb_Athamap_20091028_ 24 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 20 0 ; TOTAL 69 0 ; Host name rsat ; Job started 2026-08-17.132641 ; Job done 2026-08-17.132642 ; Seconds 0.44 ; user 0.44 ; system 0.04 ; cuser 0.87 ; csystem 0.05