; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.132843_T7oJ4S.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_2026-08-17.132843_cKlOxz.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.132843_cKlOxz.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_2026-08-17.132843_T7oJ4S.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 AT3G05815 limit START_END D -500 -1 . 0 0 0 0 AT5G42290 limit START_END D -500 -1 . 0 0 0 0 AT3G02055 limit START_END D -500 -1 . 0 0 0 0 AT5G38020 limit START_END D -500 -1 . 0 0 0 0 AT1G36580 limit START_END D -500 -1 . 0 0 0 0 BRXL4 limit START_END D -500 -1 . 0 0 0 0 AT1G16640 limit START_END D -500 -1 . 0 0 0 0 UXT2 limit START_END D -500 -1 . 0 0 0 0 AT5G50450 limit START_END D -500 -1 . 0 0 0 0 ATPLC8 limit START_END D -500 -1 . 0 0 0 0 LECRK43 limit START_END D -500 -1 . 0 0 0 0 AT3G04585 limit START_END D -500 -1 . 0 0 0 0 AT5G37000 limit START_END D -500 -1 . 0 0 0 0 AT5G24870 limit START_END D -500 -1 . 0 0 0 0 LCR84 limit START_END D -500 -1 . 0 0 0 0 AT1G06500 limit START_END D -500 -1 . 0 0 0 0 AT4G32920 limit START_END D -500 -1 . 0 0 0 0 AT1G71350 limit START_END D -500 -1 . 0 0 0 0 PRO2 limit START_END D -500 -1 . 0 0 0 0 CYP90A1 limit START_END D -500 -1 . 0 0 0 0 AT1G68430 limit START_END D -500 -1 . 0 0 0 0 AT5G45455 limit START_END D -500 -1 . 0 0 0 0 JAL36 limit START_END D -500 -1 . 0 0 0 0 AT4G12170 limit START_END D -500 -1 . 0 0 0 0 AT3G05815 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -124 -117 GTTCCCAC 5.1 6.7e-04 -7.308 3.174 AT5G42290 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -78 -71 TTGCCCAC 4.7 9.5e-04 -6.959 3.022 AT3G02055 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -483 -476 TATCCCGT 5.4 4.2e-04 -7.775 3.377 AT1G36580 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -494 -487 ATTCCCGA 6.7 2.5e-04 -8.294 3.602 AT1G36580 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -115 -108 TTGCCAGC 5.0 8.0e-04 -7.131 3.097 AT1G36580 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -66 -59 TTGCCAGC 5.0 8.0e-04 -7.131 3.097 AT1G16640 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -436 -429 AATCTCGC 4.8 8.8e-04 -7.036 3.056 AT1G16640 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -348 -341 ATCACCGC 4.8 9.5e-04 -6.959 3.022 ATPLC8 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -371 -364 TTTCCAGC 7.1 1.4e-04 -8.874 3.854 ATPLC8 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -353 -346 TTTCCCGT 7.2 1.4e-04 -8.874 3.854 ATPLC8 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -336 -329 TTTCCCAC 6.9 2.1e-04 -8.468 3.678 ATPLC8 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -317 -310 TTTCCCGG 7.0 1.6e-04 -8.740 3.796 ATPLC8 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -10 -3 TATCACGC 5.6 3.5e-04 -7.958 3.456 AT3G04585 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -188 -181 TTACCCGG 5.1 6.7e-04 -7.308 3.174 AT1G06500 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -477 -470 ATTCTCGC 7.1 1.4e-04 -8.874 3.854 AT1G06500 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -471 -464 TTTCCGGC 7.2 1.0e-04 -9.210 4.000 AT1G71350 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -374 -367 TATGCCGC 5.6 3.5e-04 -7.958 3.456 AT1G71350 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -217 -210 TATCCCAC 5.1 6.7e-04 -7.308 3.174 CYP90A1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -297 -290 TTACCAGC 5.2 5.9e-04 -7.435 3.229 JAL36 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -295 -288 TATCACGC 5.6 3.5e-04 -7.958 3.456 AT4G12170 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -229 -222 ACTACCGC 5.1 6.7e-04 -7.308 3.174 AT4G12170 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -131 -124 TTTCCCGT 7.2 1.4e-04 -8.874 3.854 AT3G05815 site 5015_E2Fb_Athamap_20091028_ R -124 -117 GTTCCCAC 5.0 6.9e-04 -7.279 3.161 AT5G42290 site 5015_E2Fb_Athamap_20091028_ D -78 -71 TTGCCCAC 4.7 8.2e-04 -7.106 3.086 AT3G02055 site 5015_E2Fb_Athamap_20091028_ D -483 -476 TATCCCGT 5.4 4.4e-04 -7.729 3.357 AT1G36580 site 5015_E2Fb_Athamap_20091028_ R -494 -487 ATTCCCGA 6.6 2.4e-04 -8.335 3.620 AT1G36580 site 5015_E2Fb_Athamap_20091028_ D -115 -108 TTGCCAGC 4.9 6.9e-04 -7.279 3.161 AT1G36580 site 5015_E2Fb_Athamap_20091028_ D -66 -59 TTGCCAGC 4.9 6.9e-04 -7.279 3.161 ATPLC8 site 5015_E2Fb_Athamap_20091028_ R -371 -364 TTTCCAGC 7.3 1.3e-04 -8.948 3.886 ATPLC8 site 5015_E2Fb_Athamap_20091028_ R -353 -346 TTTCCCGT 7.4 1.3e-04 -8.948 3.886 ATPLC8 site 5015_E2Fb_Athamap_20091028_ R -336 -329 TTTCCCAC 7.1 1.7e-04 -8.680 3.770 ATPLC8 site 5015_E2Fb_Athamap_20091028_ R -317 -310 TTTCCCGG 7.2 1.4e-04 -8.874 3.854 ATPLC8 site 5015_E2Fb_Athamap_20091028_ R -10 -3 TATCACGC 5.6 3.3e-04 -8.016 3.481 AT3G04585 site 5015_E2Fb_Athamap_20091028_ R -188 -181 TTACCCGG 5.1 6.5e-04 -7.339 3.187 AT5G24870 site 5015_E2Fb_Athamap_20091028_ D -67 -60 TTTAACGC 4.5 9.4e-04 -6.970 3.027 AT1G06500 site 5015_E2Fb_Athamap_20091028_ D -477 -470 ATTCTCGC 6.9 1.9e-04 -8.568 3.721 AT1G06500 site 5015_E2Fb_Athamap_20091028_ R -471 -464 TTTCCGGC 7.4 9.3e-05 -9.283 4.032 AT1G71350 site 5015_E2Fb_Athamap_20091028_ D -374 -367 TATGCCGC 5.5 3.6e-04 -7.929 3.444 AT1G71350 site 5015_E2Fb_Athamap_20091028_ R -217 -210 TATCCCAC 5.1 6.5e-04 -7.339 3.187 CYP90A1 site 5015_E2Fb_Athamap_20091028_ D -297 -290 TTACCAGC 5.1 5.8e-04 -7.452 3.237 JAL36 site 5015_E2Fb_Athamap_20091028_ R -295 -288 TATCACGC 5.6 3.3e-04 -8.016 3.481 AT4G12170 site 5015_E2Fb_Athamap_20091028_ R -229 -222 ACTACCGC 4.7 7.9e-04 -7.143 3.102 AT4G12170 site 5015_E2Fb_Athamap_20091028_ R -131 -124 TTTCCCGT 7.4 1.3e-04 -8.948 3.886 AT1G36580 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -498 -488 TTCCCGAGTTA 5.3 4.6e-04 -7.684 3.337 AT1G36580 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -488 -478 ATCCAGCGGAA 4.5 9.8e-04 -6.928 3.009 AT1G36580 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -375 -365 AACCTGCGATT 4.9 6.5e-04 -7.339 3.187 AT1G16640 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -440 -430 ATCTCGCTCTC 4.5 9.1e-04 -7.002 3.041 AT1G16640 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -78 -68 ATACAGCCCAA 4.6 8.3e-04 -7.094 3.081 ATPLC8 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -375 -365 TTCCAGCAAAA 5.3 4.6e-04 -7.684 3.337 ATPLC8 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -357 -347 TTCCCGTAATA 5.8 3.1e-04 -8.079 3.509 ATPLC8 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -340 -330 TTCCCACCAAA 8.1 3.9e-05 -10.152 4.409 ATPLC8 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -321 -311 TTCCCGGTCAA 7.2 1.0e-04 -9.210 4.000 AT1G06500 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -476 -466 TTCTCGCCGGA 4.7 7.7e-04 -7.169 3.114 AT1G06500 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -475 -465 TTCCGGCGAGA 5.8 3.1e-04 -8.079 3.509 AT1G71350 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -374 -364 TTAGCGGCATA 4.5 9.8e-04 -6.928 3.009 PRO2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -176 -166 AACCCGAGAAA 5.3 4.6e-04 -7.684 3.337 CYP90A1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -296 -286 TACCAGCAAAT 4.4 9.8e-04 -6.928 3.009 JAL36 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -299 -289 ATCACGCCTTA 5.7 3.3e-04 -8.016 3.481 ; ; 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_ 22 0 ; 2 5015_E2Fb_Athamap_20091028_ 21 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 15 0 ; TOTAL 58 0 ; Host name rsat ; Job started 2026-08-17.132843 ; Job done 2026-08-17.132844 ; Seconds 0.45 ; user 0.45 ; system 0.04 ; cuser 0.76 ; csystem 0.12