; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.133257_ETTfPM.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_2026-08-17.133257_GhZv43.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; bg $RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.60/oligo-frequencies/2nt_upstream-noorf_Arabidopsis_thaliana.TAIR10.60-ovlp-1str.freq ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.133257_GhZv43.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.133257_ETTfPM.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 AT1G09817 limit START_END D -500 -1 . 0 0 0 0 GTC2 limit START_END D -500 -1 . 0 0 0 0 FLC limit START_END D -500 -1 . 0 0 0 0 AT2G07659 limit START_END D -500 -1 . 0 0 0 0 AT5G40270 limit START_END D -500 -1 . 0 0 0 0 AT5G04600 limit START_END D -500 -1 . 0 0 0 0 MIK1 limit START_END D -500 -1 . 0 0 0 0 AT4G39363 limit START_END D -500 -1 . 0 0 0 0 CDA8 limit START_END D -500 -1 . 0 0 0 0 AT4G04745 limit START_END D -500 -1 . 0 0 0 0 AT1G43320 limit START_END D -500 -1 . 0 0 0 0 AT5G38580 limit START_END D -500 -1 . 0 0 0 0 AT3G57965 limit START_END D -500 -1 . 0 0 0 0 ABCG2 limit START_END D -500 -1 . 0 0 0 0 AT5G09645 limit START_END D -500 -1 . 0 0 0 0 AT2G14800 limit START_END D -500 -1 . 0 0 0 0 AT5G53500 limit START_END D -500 -1 . 0 0 0 0 UBC19 limit START_END D -500 -1 . 0 0 0 0 CUL1 limit START_END D -500 -1 . 0 0 0 0 AT3G27150 limit START_END D -500 -1 . 0 0 0 0 AT2G04870 limit START_END D -500 -1 . 0 0 0 0 EIF(ISO)4E limit START_END D -500 -1 . 0 0 0 0 FKBP16-4 limit START_END D -500 -1 . 0 0 0 0 APF1 limit START_END D -500 -1 . 0 0 0 0 AT1G09817 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -298 -291 TTACACGC 5.5 3.9e-04 -7.849 3.409 FLC site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -481 -474 TCTCCCGA 5.1 6.7e-04 -7.308 3.174 FLC site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -152 -145 TGTACCGC 5.5 3.9e-04 -7.849 3.409 FLC site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -76 -69 TTACCCCC 4.8 8.8e-04 -7.036 3.056 AT2G07659 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -400 -393 ATTCCCAC 6.5 2.7e-04 -8.217 3.569 AT2G07659 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -365 -358 CTTCCCCC 4.9 8.0e-04 -7.131 3.097 AT2G07659 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -281 -274 ATACGCGC 5.5 3.9e-04 -7.849 3.409 AT2G07659 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -134 -127 CTTCCCTC 5.2 5.9e-04 -7.435 3.229 AT5G04600 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -341 -334 TTTCCGGC 7.2 1.0e-04 -9.210 4.000 MIK1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -308 -301 TTTCCCAC 6.9 2.1e-04 -8.468 3.678 AT5G38580 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -244 -237 TTGCCAGC 5.0 8.0e-04 -7.131 3.097 AT5G38580 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -171 -164 TTTCCAGC 7.1 1.4e-04 -8.874 3.854 AT5G38580 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -152 -145 TGTCCAGC 5.0 7.4e-04 -7.209 3.131 AT3G57965 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -189 -182 TGTCCCGC 8.1 2.3e-05 -10.680 4.638 ABCG2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -406 -399 TTTGCCGC 7.3 7.6e-05 -9.485 4.119 AT5G09645 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -288 -281 TGTCCCGT 5.1 6.7e-04 -7.308 3.174 AT2G14800 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -352 -345 ATGTCCGC 4.8 9.5e-04 -6.959 3.022 AT2G14800 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -305 -298 TTTCCAGC 7.1 1.4e-04 -8.874 3.854 AT2G14800 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -119 -112 TGTCCCAC 4.8 8.8e-04 -7.036 3.056 AT5G53500 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -116 -109 ATTCCCTC 6.6 2.6e-04 -8.255 3.585 UBC19 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -424 -417 TCTCCCTC 4.9 8.0e-04 -7.131 3.097 UBC19 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -226 -219 ATACCCTC 4.7 9.5e-04 -6.959 3.022 UBC19 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -72 -65 ATAGCCGC 5.2 5.9e-04 -7.435 3.229 CUL1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -403 -396 TTACCGGC 5.3 5.1e-04 -7.581 3.292 CUL1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -264 -257 ATGGCCGC 4.7 9.5e-04 -6.959 3.022 AT3G27150 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -264 -257 TTCCACGC 5.1 6.7e-04 -7.308 3.174 AT2G04870 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -458 -451 TGTCCCAC 4.8 8.8e-04 -7.036 3.056 AT2G04870 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -423 -416 TGTCCCAC 4.8 8.8e-04 -7.036 3.056 FKBP16-4 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -461 -454 TGTCCCGA 5.0 7.4e-04 -7.209 3.131 APF1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -73 -66 TTACCTGC 5.2 5.9e-04 -7.435 3.229 AT1G09817 site 5015_E2Fb_Athamap_20091028_ R -298 -291 TTACACGC 5.5 3.9e-04 -7.849 3.409 AT1G09817 site 5015_E2Fb_Athamap_20091028_ D -137 -130 TTGCCCCC 4.5 9.4e-04 -6.970 3.027 FLC site 5015_E2Fb_Athamap_20091028_ D -481 -474 TCTCCCGA 5.0 6.5e-04 -7.339 3.187 FLC site 5015_E2Fb_Athamap_20091028_ R -152 -145 TGTACCGC 5.5 3.9e-04 -7.849 3.409 FLC site 5015_E2Fb_Athamap_20091028_ D -76 -69 TTACCCCC 4.7 7.9e-04 -7.143 3.102 AT2G07659 site 5015_E2Fb_Athamap_20091028_ R -400 -393 ATTCCCAC 6.3 2.7e-04 -8.217 3.569 AT2G07659 site 5015_E2Fb_Athamap_20091028_ R -365 -358 CTTCCCCC 4.8 7.9e-04 -7.143 3.102 AT2G07659 site 5015_E2Fb_Athamap_20091028_ D -281 -274 ATACGCGC 5.1 6.5e-04 -7.339 3.187 AT2G07659 site 5015_E2Fb_Athamap_20091028_ R -134 -127 CTTCCCTC 5.0 6.5e-04 -7.339 3.187 AT5G04600 site 5015_E2Fb_Athamap_20091028_ R -341 -334 TTTCCGGC 7.4 9.3e-05 -9.283 4.032 MIK1 site 5015_E2Fb_Athamap_20091028_ R -334 -327 TTTAACGC 4.5 9.4e-04 -6.970 3.027 MIK1 site 5015_E2Fb_Athamap_20091028_ R -308 -301 TTTCCCAC 7.1 1.7e-04 -8.680 3.770 AT5G38580 site 5015_E2Fb_Athamap_20091028_ D -244 -237 TTGCCAGC 4.9 6.9e-04 -7.279 3.161 AT5G38580 site 5015_E2Fb_Athamap_20091028_ D -171 -164 TTTCCAGC 7.3 1.3e-04 -8.948 3.886 AT5G38580 site 5015_E2Fb_Athamap_20091028_ D -152 -145 TGTCCAGC 4.9 6.9e-04 -7.279 3.161 AT3G57965 site 5015_E2Fb_Athamap_20091028_ R -189 -182 TGTCCCGC 8.3 2.3e-05 -10.680 4.638 ABCG2 site 5015_E2Fb_Athamap_20091028_ D -406 -399 TTTGCCGC 7.5 6.2e-05 -9.688 4.208 AT5G09645 site 5015_E2Fb_Athamap_20091028_ R -288 -281 TGTCCCGT 5.0 6.5e-04 -7.339 3.187 AT2G14800 site 5015_E2Fb_Athamap_20091028_ R -305 -298 TTTCCAGC 7.3 1.3e-04 -8.948 3.886 AT2G14800 site 5015_E2Fb_Athamap_20091028_ R -119 -112 TGTCCCAC 4.7 7.9e-04 -7.143 3.102 AT5G53500 site 5015_E2Fb_Athamap_20091028_ R -116 -109 ATTCCCTC 6.4 2.6e-04 -8.255 3.585 UBC19 site 5015_E2Fb_Athamap_20091028_ D -424 -417 TCTCCCTC 4.8 7.5e-04 -7.195 3.125 UBC19 site 5015_E2Fb_Athamap_20091028_ D -72 -65 ATAGCCGC 4.8 7.9e-04 -7.143 3.102 CUL1 site 5015_E2Fb_Athamap_20091028_ R -403 -396 TTACCGGC 5.3 5.1e-04 -7.581 3.292 AT3G27150 site 5015_E2Fb_Athamap_20091028_ D -264 -257 TTCCACGC 5.1 6.5e-04 -7.339 3.187 AT2G04870 site 5015_E2Fb_Athamap_20091028_ D -458 -451 TGTCCCAC 4.7 7.9e-04 -7.143 3.102 AT2G04870 site 5015_E2Fb_Athamap_20091028_ D -423 -416 TGTCCCAC 4.7 7.9e-04 -7.143 3.102 FKBP16-4 site 5015_E2Fb_Athamap_20091028_ R -461 -454 TGTCCCGA 5.0 6.9e-04 -7.279 3.161 APF1 site 5015_E2Fb_Athamap_20091028_ D -73 -66 TTACCTGC 5.1 5.8e-04 -7.452 3.237 AT1G09817 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -312 -302 TTCTCGTCCTT 5.2 5.0e-04 -7.601 3.301 AT1G09817 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -229 -219 TTCCCATCAAT 4.6 9.1e-04 -7.002 3.041 FLC site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -231 -221 TTCCTCCCCTA 5.1 5.4e-04 -7.524 3.268 FLC site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -76 -66 TTACCCCCAAA 4.8 7.2e-04 -7.236 3.143 AT2G07659 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -404 -394 TTCCCACACAT 5.5 3.9e-04 -7.849 3.409 AT2G07659 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -281 -271 AGCGCGCGTAT 5.1 5.4e-04 -7.524 3.268 AT2G07659 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -280 -270 TACGCGCGCTG 7.8 5.3e-05 -9.845 4.276 AT2G07659 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -269 -259 TCAGCGCCCTA 5.5 3.9e-04 -7.849 3.409 AT2G07659 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -207 -197 TACGCTCTCTT 5.0 6.0e-04 -7.419 3.222 AT2G07659 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -138 -128 TTCCCTCTCAT 7.0 1.2e-04 -9.028 3.921 AT5G04600 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -345 -335 TTCCGGCGAGT 5.5 3.9e-04 -7.849 3.409 MIK1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -312 -302 TTCCCACCTTT 5.3 5.0e-04 -7.601 3.301 AT4G39363 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -60 -50 TTCCCATCATA 4.9 6.5e-04 -7.339 3.187 AT4G04745 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -84 -74 TTCAAGCCAAT 4.9 6.5e-04 -7.339 3.187 AT5G38580 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -170 -160 TTCCAGCTATC 4.8 7.2e-04 -7.236 3.143 ABCG2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -398 -388 ATCGTGCCAAA 6.4 1.9e-04 -8.568 3.721 AT2G14800 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -309 -299 TTCCAGCCGTT 5.8 3.1e-04 -8.079 3.509 AT5G53500 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -372 -362 TACGCGGCATG 4.5 9.1e-04 -7.002 3.041 AT5G53500 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -120 -110 TTCCCTCTGTA 4.6 9.1e-04 -7.002 3.041 UBC19 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -71 -61 TAGCCGCTATA 6.9 1.4e-04 -8.874 3.854 CUL1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -434 -424 AACCCACCATT 5.3 4.6e-04 -7.684 3.337 CUL1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -424 -414 TTCTTGCGCAA 4.9 6.5e-04 -7.339 3.187 CUL1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -407 -397 TACCGGCGTTA 4.8 7.2e-04 -7.236 3.143 CUL1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -273 -263 AACGCGTCCAT 5.7 3.6e-04 -7.929 3.444 EIF(ISO)4E site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -247 -237 ATTCCGCTATT 5.8 3.3e-04 -8.016 3.481 EIF(ISO)4E site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -31 -21 GACCGGCCCAA 5.2 5.0e-04 -7.601 3.301 FKBP16-4 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -224 -214 TTCTCACCAAA 5.1 6.0e-04 -7.419 3.222 APF1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -487 -477 TACACGCTCTC 4.6 8.3e-04 -7.094 3.081 APF1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -72 -62 TACCTGCCATC 5.2 5.0e-04 -7.601 3.301 APF1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -11 -1 TTCCCGAAAAT 5.1 5.4e-04 -7.524 3.268 ; ; 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_ 30 0 ; 2 5015_E2Fb_Athamap_20091028_ 29 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 30 0 ; TOTAL 89 0 ; Host name rsat ; Job started 2026-08-17.133257 ; Job done 2026-08-17.133258 ; Seconds 0.48 ; user 0.49 ; system 0.05 ; cuser 0.81 ; csystem 0.11