; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.163537_Mu7e9A.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_2026-08-17.163537_1J31ve.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.163537_1J31ve.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_2026-08-17.163537_Mu7e9A.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 AT5G43310 limit START_END D -500 -1 . 0 0 0 0 AT3G15040 limit START_END D -500 -1 . 0 0 0 0 AT2G23200 limit START_END D -500 -1 . 0 0 0 0 AT3G01820 limit START_END D -500 -1 . 0 0 0 0 AT5G01070 limit START_END D -500 -1 . 0 0 0 0 ATJ8 limit START_END D -500 -1 . 0 0 0 0 AT1G76954 limit START_END D -500 -1 . 0 0 0 0 AMR1 limit START_END D -500 -1 . 0 0 0 0 AT5G53920 limit START_END D -500 -1 . 0 0 0 0 SHT limit START_END D -500 -1 . 0 0 0 0 FAMA limit START_END D -500 -1 . 0 0 0 0 AT3G11300 limit START_END D -500 -1 . 0 0 0 0 AT1G09957 limit START_END D -500 -1 . 0 0 0 0 GAUT7 limit START_END D -500 -1 . 0 0 0 0 AT1G57775 limit START_END D -500 -1 . 0 0 0 0 AT3G04935 limit START_END D -500 -1 . 0 0 0 0 AT2G33735 limit START_END D -500 -1 . 0 0 0 0 AT1G64050 limit START_END D -500 -1 . 0 0 0 0 AT3G42850 limit START_END D -500 -1 . 0 0 0 0 AT5G38820 limit START_END D -500 -1 . 0 0 0 0 VOZ2 limit START_END D -500 -1 . 0 0 0 0 AT2G19550 limit START_END D -500 -1 . 0 0 0 0 ESFL3 limit START_END D -500 -1 . 0 0 0 0 LSM5 limit START_END D -500 -1 . 0 0 0 0 HRE1 limit START_END D -500 -1 . 0 0 0 0 ERF104 limit START_END D -500 -1 . 0 0 0 0 SWI2 limit START_END D -500 -1 . 0 0 0 0 AT4G03120 limit START_END D -500 -1 . 0 0 0 0 AT5G43310 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -197 -190 TTTCCAGC 7.1 1.4e-04 -8.874 3.854 AT5G43310 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -28 -21 TTACCCCC 4.8 8.8e-04 -7.036 3.056 AT2G23200 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -468 -461 TGTCCCGG 4.9 8.0e-04 -7.131 3.097 AT2G23200 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -121 -114 TGTCCCGT 5.1 6.7e-04 -7.308 3.174 AT3G01820 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -365 -358 TCTCTCGC 5.4 4.2e-04 -7.775 3.377 AT3G01820 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -182 -175 GTTCCCGC 8.4 1.5e-05 -11.107 4.824 AT5G01070 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -434 -427 TTTCACGC 7.4 6.6e-05 -9.626 4.180 ATJ8 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -386 -379 ATTCACGC 7.0 1.6e-04 -8.740 3.796 AT5G53920 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -466 -459 ATGCACGC 4.9 8.0e-04 -7.131 3.097 FAMA site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -479 -472 TTTCCCAC 6.9 2.1e-04 -8.468 3.678 AT3G11300 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -108 -101 TTTCCCCC 6.7 2.5e-04 -8.294 3.602 AT3G11300 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -106 -99 TCCCCCGC 5.7 3.4e-04 -7.987 3.469 AT1G57775 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -412 -405 TATCCCTC 5.2 5.9e-04 -7.435 3.229 AT3G04935 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -421 -414 TTACCCAC 5.0 7.4e-04 -7.209 3.131 AT3G04935 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -131 -124 TTACCTGC 5.2 5.9e-04 -7.435 3.229 AT2G33735 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -11 -4 ATTACCGC 7.2 1.0e-04 -9.210 4.000 AT3G42850 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -329 -322 TTACCTGC 5.2 5.9e-04 -7.435 3.229 AT2G19550 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -415 -408 CTTCCCGT 5.4 4.2e-04 -7.775 3.377 AT2G19550 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -102 -95 ACTCTCGC 5.0 8.0e-04 -7.131 3.097 HRE1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -453 -446 ATTCCCGC 9.8 8.5e-06 -11.675 5.071 HRE1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -443 -436 TATACCGC 5.9 3.1e-04 -8.079 3.509 HRE1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -437 -430 TAACCCGC 6.1 3.0e-04 -8.112 3.523 AT4G03120 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -479 -472 AGTCACGC 4.9 8.0e-04 -7.131 3.097 AT4G03120 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -149 -142 CTCCCCGC 6.2 2.9e-04 -8.146 3.538 AT5G43310 site 5015_E2Fb_Athamap_20091028_ R -197 -190 TTTCCAGC 7.3 1.3e-04 -8.948 3.886 AT5G43310 site 5015_E2Fb_Athamap_20091028_ D -28 -21 TTACCCCC 4.7 7.9e-04 -7.143 3.102 AT5G43310 site 5015_E2Fb_Athamap_20091028_ D -15 -8 TTTCGCGA 4.5 9.4e-04 -6.970 3.027 AT2G23200 site 5015_E2Fb_Athamap_20091028_ D -468 -461 TGTCCCGG 4.9 7.5e-04 -7.195 3.125 AT2G23200 site 5015_E2Fb_Athamap_20091028_ R -121 -114 TGTCCCGT 5.0 6.5e-04 -7.339 3.187 AT3G01820 site 5015_E2Fb_Athamap_20091028_ R -365 -358 TCTCTCGC 5.4 4.4e-04 -7.729 3.357 AT3G01820 site 5015_E2Fb_Athamap_20091028_ D -216 -209 TTTACGGC 4.5 9.4e-04 -6.970 3.027 AT3G01820 site 5015_E2Fb_Athamap_20091028_ D -182 -175 GTTCCCGC 8.6 1.5e-05 -11.107 4.824 AT5G01070 site 5015_E2Fb_Athamap_20091028_ R -434 -427 TTTCACGC 7.6 5.8e-05 -9.755 4.237 ATJ8 site 5015_E2Fb_Athamap_20091028_ R -386 -379 ATTCACGC 6.9 1.9e-04 -8.568 3.721 AT5G53920 site 5015_E2Fb_Athamap_20091028_ D -466 -459 ATGCACGC 4.5 9.4e-04 -6.970 3.027 FAMA site 5015_E2Fb_Athamap_20091028_ D -479 -472 TTTCCCAC 7.1 1.7e-04 -8.680 3.770 AT3G11300 site 5015_E2Fb_Athamap_20091028_ D -108 -101 TTTCCCCC 6.9 1.9e-04 -8.568 3.721 AT3G11300 site 5015_E2Fb_Athamap_20091028_ D -106 -99 TCCCCCGC 5.6 3.3e-04 -8.016 3.481 AT1G57775 site 5015_E2Fb_Athamap_20091028_ D -412 -405 TATCCCTC 5.1 5.8e-04 -7.452 3.237 AT3G04935 site 5015_E2Fb_Athamap_20091028_ D -421 -414 TTACCCAC 4.9 6.9e-04 -7.279 3.161 AT3G04935 site 5015_E2Fb_Athamap_20091028_ R -131 -124 TTACCTGC 5.1 5.8e-04 -7.452 3.237 AT2G33735 site 5015_E2Fb_Athamap_20091028_ D -11 -4 ATTACCGC 7.1 1.7e-04 -8.680 3.770 AT3G42850 site 5015_E2Fb_Athamap_20091028_ R -329 -322 TTACCTGC 5.1 5.8e-04 -7.452 3.237 AT2G19550 site 5015_E2Fb_Athamap_20091028_ R -415 -408 CTTCCCGT 5.3 5.1e-04 -7.581 3.292 AT2G19550 site 5015_E2Fb_Athamap_20091028_ R -102 -95 ACTCTCGC 4.5 9.4e-04 -6.970 3.027 HRE1 site 5015_E2Fb_Athamap_20091028_ D -453 -446 ATTCCCGC 10.0 8.5e-06 -11.675 5.071 HRE1 site 5015_E2Fb_Athamap_20091028_ D -443 -436 TATACCGC 5.8 3.1e-04 -8.079 3.509 HRE1 site 5015_E2Fb_Athamap_20091028_ R -437 -430 TAACCCGC 6.0 2.9e-04 -8.146 3.538 AT4G03120 site 5015_E2Fb_Athamap_20091028_ D -479 -472 AGTCACGC 4.5 9.4e-04 -6.970 3.027 AT4G03120 site 5015_E2Fb_Athamap_20091028_ R -149 -142 CTCCCCGC 6.1 2.9e-04 -8.146 3.538 AT5G43310 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -500 -490 ATCACGCTCCA 4.6 8.3e-04 -7.094 3.081 AT5G43310 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -478 -468 TACTCACCATA 4.5 9.1e-04 -7.002 3.041 AT5G43310 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -128 -118 TTCGAGCCAAT 7.3 9.0e-05 -9.316 4.046 AT5G43310 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -28 -18 TTACCCCCAAA 4.8 7.2e-04 -7.236 3.143 AT5G43310 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -14 -4 TTCGCGATATT 5.9 2.9e-04 -8.146 3.538 AT3G01820 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -369 -359 CTCTCGCTCAA 5.5 3.9e-04 -7.849 3.409 AT3G01820 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -215 -205 TTACGGCGCTA 5.3 4.6e-04 -7.684 3.337 AT3G01820 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -181 -171 TTCCCGCGGCT 6.7 1.5e-04 -8.805 3.824 AT5G01070 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -438 -428 TTCACGCCACC 4.5 9.1e-04 -7.002 3.041 AT5G01070 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -199 -189 TCCGCACGCTA 4.8 7.2e-04 -7.236 3.143 ATJ8 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -390 -380 TTCACGCTAAA 7.6 6.6e-05 -9.626 4.180 AT1G76954 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -341 -331 TCACCGCTATA 5.1 5.4e-04 -7.524 3.268 SHT site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -193 -183 ATCACGCGTAT 5.2 5.0e-04 -7.601 3.301 SHT site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -23 -13 TTCGTGCTAAA 6.2 2.5e-04 -8.294 3.602 FAMA site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -478 -468 TTCCCACGATT 7.0 1.2e-04 -9.028 3.921 FAMA site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -142 -132 TTCACACCCTA 5.5 3.9e-04 -7.849 3.409 AT3G11300 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -107 -97 TTCCCCCGCTT 7.2 1.0e-04 -9.210 4.000 AT1G09957 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -66 -56 AACCTGCTAAA 4.8 7.2e-04 -7.236 3.143 AT3G04935 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -135 -125 TACCTGCAAAT 4.4 9.8e-04 -6.928 3.009 AT3G42850 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -367 -357 TTTTCGCCATA 5.3 4.6e-04 -7.684 3.337 AT2G19550 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -106 -96 CTCTCGCCAAA 6.5 1.8e-04 -8.623 3.745 HRE1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -453 -443 ATCGCGGGAAT 5.4 4.2e-04 -7.775 3.377 HRE1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -452 -442 TTCCCGCGATA 11.5 7.0e-07 -14.172 6.155 HRE1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -441 -431 AACCCGCGGTA 6.8 1.4e-04 -8.874 3.854 SWI2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -209 -199 TTCTCGTGCAT 4.8 7.2e-04 -7.236 3.143 AT4G03120 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -451 -441 ATTCCGCTAAT 6.1 2.5e-04 -8.294 3.602 AT4G03120 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -415 -405 ATTCCGCCGTT 4.9 6.5e-04 -7.339 3.187 AT4G03120 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -355 -345 ATTCCGCGACA 4.8 7.7e-04 -7.169 3.114 AT4G03120 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -353 -343 TCCGCGACATT 4.7 7.7e-04 -7.169 3.114 AT4G03120 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -344 -334 TTTCAGCCAAA 4.8 7.2e-04 -7.236 3.143 AT4G03120 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -153 -143 TCCCCGCCGGT 5.0 6.5e-04 -7.339 3.187 ; ; 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 28 ; Sum of sequence lengths 14000 ; N residues 0 ; Matches per matrix ; matrix name matches scored ; 1 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ 24 0 ; 2 5015_E2Fb_Athamap_20091028_ 26 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 31 0 ; TOTAL 81 0 ; Host name rsat ; Job started 2026-08-17.163538 ; Job done 2026-08-17.163539 ; Seconds 0.46 ; user 0.46 ; system 0.04 ; cuser 0.82 ; csystem 0.09