; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.110607_JCO9ew.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_2026-08-17.110607_HOUQmM.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.110607_HOUQmM.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_2026-08-17.110607_JCO9ew.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 AT5G01665|AT5G01665 limit START_END D -500 -1 . 0 0 0 0 AT1G76440|AT1G76440 limit START_END D -500 -1 . 0 0 0 0 AT1G17150|AT1G17150 limit START_END D -500 -1 . 0 0 0 0 AT5G49140|AT5G49140 limit START_END D -500 -1 . 0 0 0 0 AT5G66750|DDM1 limit START_END D -500 -1 . 0 0 0 0 AT3G04195|AT3G04195 limit START_END D -500 -1 . 0 0 0 0 AT5G36739|AT5G36739 limit START_END D -500 -1 . 0 0 0 0 AT2G18480|PLT3 limit START_END D -500 -1 . 0 0 0 0 AT1G25270|AT1G25270 limit START_END D -500 -1 . 0 0 0 0 AT1G61850|AT1G61850 limit START_END D -500 -1 . 0 0 0 0 AT3G62280|AT3G62280 limit START_END D -500 -1 . 0 0 0 0 AT5G58003|CPL4 limit START_END D -500 -1 . 0 0 0 0 AT1G05053|AT1G05053 limit START_END D -500 -1 . 0 0 0 0 AT1G07901|AT1G07901 limit START_END D -500 -1 . 0 0 0 0 AT2G09060|AT2G09060 limit START_END D -500 -1 . 0 0 0 0 AT1G11090|AT1G11090 limit START_END D -500 -1 . 0 0 0 0 AT5G13790|AGL15 limit START_END D -500 -1 . 0 0 0 0 AT3G55650|AT3G55650 limit START_END D -500 -1 . 0 0 0 0 AT2G36695|AT2G36695 limit START_END D -500 -1 . 0 0 0 0 AT1G43080|AT1G43080 limit START_END D -500 -1 . 0 0 0 0 AT1G63740|AT1G63740 limit START_END D -500 -1 . 0 0 0 0 AT4G09300|AT4G09300 limit START_END D -500 -1 . 0 0 0 0 AT2G04621|AT2G04621 limit START_END D -500 -1 . 0 0 0 0 AT5G01665|AT5G01665 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -186 -179 TTTCCGGC 7.2 1.0e-04 -9.210 4.000 AT5G01665|AT5G01665 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -163 -156 ATGGCCGC 4.7 9.5e-04 -6.959 3.022 AT1G76440|AT1G76440 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -211 -204 TTACCTGC 5.2 5.9e-04 -7.435 3.229 AT5G66750|DDM1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -499 -492 TTTCCCGC 10.2 4.7e-06 -12.268 5.328 AT5G66750|DDM1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -33 -26 CTTCCCGC 8.5 1.5e-05 -11.107 4.824 AT3G04195|AT3G04195 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -228 -221 TTACCCAC 5.0 7.4e-04 -7.209 3.131 AT3G04195|AT3G04195 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -130 -123 TCTCCCTC 4.9 8.0e-04 -7.131 3.097 AT3G04195|AT3G04195 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -35 -28 TATCCCCC 4.9 8.0e-04 -7.131 3.097 AT1G61850|AT1G61850 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -464 -457 TCTCCCAC 4.9 8.8e-04 -7.036 3.056 AT3G62280|AT3G62280 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -475 -468 TATCCCTC 5.2 5.9e-04 -7.435 3.229 AT3G62280|AT3G62280 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -441 -434 TTCCCCGG 4.7 9.5e-04 -6.959 3.022 AT3G62280|AT3G62280 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -291 -284 ATTCTCGC 7.1 1.4e-04 -8.874 3.854 AT3G62280|AT3G62280 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -233 -226 ATCCCCGC 7.6 4.7e-05 -9.965 4.328 AT3G62280|AT3G62280 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -176 -169 ATCCACGC 4.8 9.5e-04 -6.959 3.022 AT5G58003|CPL4 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -44 -37 AGGCCCGC 5.4 4.2e-04 -7.775 3.377 AT1G05053|AT1G05053 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -114 -107 TTGCCGGC 5.1 7.4e-04 -7.209 3.131 AT1G05053|AT1G05053 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -112 -105 ATGCCGGC 4.7 9.5e-04 -6.959 3.022 AT1G11090|AT1G11090 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -415 -408 ATTCACGC 7.0 1.6e-04 -8.740 3.796 AT1G11090|AT1G11090 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -379 -372 ATACACGC 5.2 6.7e-04 -7.308 3.174 AT1G11090|AT1G11090 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -181 -174 ATTCCCCC 6.3 2.9e-04 -8.146 3.538 AT3G55650|AT3G55650 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -424 -417 CTTCCCGA 5.3 5.1e-04 -7.581 3.292 AT3G55650|AT3G55650 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -102 -95 TTCCCTGC 4.8 8.8e-04 -7.036 3.056 AT4G09300|AT4G09300 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -99 -92 TTCCCCGA 4.8 8.8e-04 -7.036 3.056 AT4G09300|AT4G09300 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -21 -14 CTTCCCCC 4.9 8.0e-04 -7.131 3.097 AT2G04621|AT2G04621 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -353 -346 TATCCCCC 4.9 8.0e-04 -7.131 3.097 AT5G01665|AT5G01665 site 5015_E2Fb_Athamap_20091028_ D -186 -179 TTTCCGGC 7.4 9.3e-05 -9.283 4.032 AT1G76440|AT1G76440 site 5015_E2Fb_Athamap_20091028_ D -211 -204 TTACCTGC 5.1 5.8e-04 -7.452 3.237 AT5G49140|AT5G49140 site 5015_E2Fb_Athamap_20091028_ D -171 -164 TTCCCCTC 4.6 8.2e-04 -7.106 3.086 AT5G66750|DDM1 site 5015_E2Fb_Athamap_20091028_ R -499 -492 TTTCCCGC 10.7 4.7e-06 -12.268 5.328 AT5G66750|DDM1 site 5015_E2Fb_Athamap_20091028_ D -33 -26 CTTCCCGC 8.6 1.5e-05 -11.107 4.824 AT3G04195|AT3G04195 site 5015_E2Fb_Athamap_20091028_ R -228 -221 TTACCCAC 4.9 6.9e-04 -7.279 3.161 AT3G04195|AT3G04195 site 5015_E2Fb_Athamap_20091028_ R -130 -123 TCTCCCTC 4.8 7.5e-04 -7.195 3.125 AT3G04195|AT3G04195 site 5015_E2Fb_Athamap_20091028_ R -35 -28 TATCCCCC 4.9 7.5e-04 -7.195 3.125 AT1G61850|AT1G61850 site 5015_E2Fb_Athamap_20091028_ R -464 -457 TCTCCCAC 4.8 7.5e-04 -7.195 3.125 AT3G62280|AT3G62280 site 5015_E2Fb_Athamap_20091028_ R -475 -468 TATCCCTC 5.1 5.8e-04 -7.452 3.237 AT3G62280|AT3G62280 site 5015_E2Fb_Athamap_20091028_ R -441 -434 TTCCCCGG 4.7 8.2e-04 -7.106 3.086 AT3G62280|AT3G62280 site 5015_E2Fb_Athamap_20091028_ D -291 -284 ATTCTCGC 6.9 1.9e-04 -8.568 3.721 AT3G62280|AT3G62280 site 5015_E2Fb_Athamap_20091028_ R -233 -226 ATCCCCGC 7.4 9.3e-05 -9.283 4.032 AT5G58003|CPL4 site 5015_E2Fb_Athamap_20091028_ R -44 -37 AGGCCCGC 5.0 6.5e-04 -7.339 3.187 AT1G05053|AT1G05053 site 5015_E2Fb_Athamap_20091028_ D -114 -107 TTGCCGGC 5.0 6.5e-04 -7.339 3.187 AT1G11090|AT1G11090 site 5015_E2Fb_Athamap_20091028_ D -415 -408 ATTCACGC 6.9 1.9e-04 -8.568 3.721 AT1G11090|AT1G11090 site 5015_E2Fb_Athamap_20091028_ D -379 -372 ATACACGC 4.7 7.9e-04 -7.143 3.102 AT1G11090|AT1G11090 site 5015_E2Fb_Athamap_20091028_ D -181 -174 ATTCCCCC 6.2 2.9e-04 -8.146 3.538 AT3G55650|AT3G55650 site 5015_E2Fb_Athamap_20091028_ D -424 -417 CTTCCCGA 5.2 5.1e-04 -7.581 3.292 AT3G55650|AT3G55650 site 5015_E2Fb_Athamap_20091028_ D -102 -95 TTCCCTGC 4.7 7.9e-04 -7.143 3.102 AT4G09300|AT4G09300 site 5015_E2Fb_Athamap_20091028_ R -99 -92 TTCCCCGA 4.8 7.9e-04 -7.143 3.102 AT4G09300|AT4G09300 site 5015_E2Fb_Athamap_20091028_ R -21 -14 CTTCCCCC 4.8 7.9e-04 -7.143 3.102 AT2G04621|AT2G04621 site 5015_E2Fb_Athamap_20091028_ R -353 -346 TATCCCCC 4.9 7.5e-04 -7.195 3.125 AT5G49140|AT5G49140 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -171 -161 TTCCCCTCCAT 4.9 6.5e-04 -7.339 3.187 AT5G49140|AT5G49140 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -170 -160 TCCCCTCCATT 5.1 5.4e-04 -7.524 3.268 AT5G66750|DDM1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -367 -357 CTCCGGCCAAT 5.9 2.9e-04 -8.146 3.538 AT5G66750|DDM1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -32 -22 TTCCCGCCCAT 12.1 2.0e-07 -15.425 6.699 AT5G66750|DDM1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -23 -13 GTAGCGCCCAT 5.6 3.6e-04 -7.929 3.444 AT3G04195|AT3G04195 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -232 -222 TACCCACAATA 4.5 9.1e-04 -7.002 3.041 AT3G04195|AT3G04195 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -134 -124 CTCCCTCGAAA 5.2 5.4e-04 -7.524 3.268 AT1G25270|AT1G25270 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -63 -53 TACCCACTCTA 6.4 1.9e-04 -8.568 3.721 AT1G25270|AT1G25270 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -32 -22 TTCGCCCCACA 5.1 5.4e-04 -7.524 3.268 AT3G62280|AT3G62280 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -290 -280 TTCTCGCTTTT 4.4 9.8e-04 -6.928 3.009 AT3G62280|AT3G62280 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -237 -227 TCCCCGCTACT 5.9 2.9e-04 -8.146 3.538 AT3G62280|AT3G62280 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -146 -136 TTCGCACTCGA 4.4 9.8e-04 -6.928 3.009 AT5G58003|CPL4 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -270 -260 TTTCCTCCATA 4.8 7.2e-04 -7.236 3.143 AT2G09060|AT2G09060 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -421 -411 AATCCGCCAAA 6.3 2.3e-04 -8.377 3.638 AT1G11090|AT1G11090 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -415 -405 ATCGCGTGAAT 5.6 3.6e-04 -7.929 3.444 AT1G11090|AT1G11090 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -414 -404 TTCACGCGATT 7.7 6.1e-05 -9.705 4.215 AT1G11090|AT1G11090 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -392 -382 TACACGCGAAT 7.3 9.0e-05 -9.316 4.046 AT5G13790|AGL15 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -205 -195 TTCCTTCCCTT 4.4 9.8e-04 -6.928 3.009 AT3G55650|AT3G55650 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -423 -413 TTCCCGATCGA 5.4 4.2e-04 -7.775 3.377 AT3G55650|AT3G55650 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -101 -91 TCCCTGCTCAT 4.6 8.3e-04 -7.094 3.081 AT1G43080|AT1G43080 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -190 -180 AAGCCGCCCAT 6.6 1.6e-04 -8.740 3.796 AT4G09300|AT4G09300 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -324 -314 ATCCCTCCATC 4.9 7.2e-04 -7.236 3.143 ; ; 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_ 23 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 22 0 ; TOTAL 70 0 ; Host name rsat ; Job started 2026-08-17.110607 ; Job done 2026-08-17.110608 ; Seconds 0.48 ; user 0.49 ; system 0.03 ; cuser 0.74 ; csystem 0.1