; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.164215_iWDdEv.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_2026-08-17.164215_pNcL4v.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.164215_pNcL4v.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_2026-08-17.164215_iWDdEv.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 AT1G53340 limit START_END D -500 -1 . 0 0 0 0 AT2G09095 limit START_END D -500 -1 . 0 0 0 0 AT4G02489 limit START_END D -500 -1 . 0 0 0 0 PER58 limit START_END D -500 -1 . 0 0 0 0 DCD limit START_END D -500 -1 . 0 0 0 0 AT4G02110 limit START_END D -500 -1 . 0 0 0 0 AT1G68960 limit START_END D -500 -1 . 0 0 0 0 GLP9 limit START_END D -500 -1 . 0 0 0 0 AT5G24040 limit START_END D -500 -1 . 0 0 0 0 AT3G54240 limit START_END D -500 -1 . 0 0 0 0 AT1G06190 limit START_END D -500 -1 . 0 0 0 0 AT4G39838 limit START_END D -500 -1 . 0 0 0 0 AT1G04837 limit START_END D -500 -1 . 0 0 0 0 AT4G17550 limit START_END D -500 -1 . 0 0 0 0 RABG3F limit START_END D -500 -1 . 0 0 0 0 AT3G18510 limit START_END D -500 -1 . 0 0 0 0 AT2G37362 limit START_END D -500 -1 . 0 0 0 0 AT4G08425 limit START_END D -500 -1 . 0 0 0 0 SAUR21 limit START_END D -500 -1 . 0 0 0 0 AT1G04787 limit START_END D -500 -1 . 0 0 0 0 POLAR limit START_END D -500 -1 . 0 0 0 0 TPK2 limit START_END D -500 -1 . 0 0 0 0 AT3G13435 limit START_END D -500 -1 . 0 0 0 0 PCMP-H52 limit START_END D -500 -1 . 0 0 0 0 AT2G33255 limit START_END D -500 -1 . 0 0 0 0 LINC4 limit START_END D -500 -1 . 0 0 0 0 AT1G01570 limit START_END D -500 -1 . 0 0 0 0 BBX23 limit START_END D -500 -1 . 0 0 0 0 AT1G53340 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -394 -387 TATCACGC 5.6 3.5e-04 -7.958 3.456 AT1G53340 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -310 -303 ATTCCGGC 6.8 2.1e-04 -8.468 3.678 AT4G02489 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -447 -440 TGTCCCGA 5.0 7.4e-04 -7.209 3.131 AT4G02489 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -416 -409 GTTCCTGC 5.3 5.1e-04 -7.581 3.292 AT4G02489 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -303 -296 TTAGCCGC 5.5 3.9e-04 -7.849 3.409 AT4G02489 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -91 -84 TCTCTCGC 5.4 4.2e-04 -7.775 3.377 AT4G02489 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -85 -78 GCTCCCGC 6.4 2.7e-04 -8.217 3.569 AT4G02489 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -60 -53 ACTCTCGC 5.0 8.0e-04 -7.131 3.097 AT4G02110 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -66 -59 TAGCCCGC 6.3 2.9e-04 -8.146 3.538 GLP9 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -118 -111 GTTCCCTC 5.2 6.7e-04 -7.308 3.174 AT1G06190 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -460 -453 TCTACCGC 5.6 3.5e-04 -7.958 3.456 AT1G06190 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -175 -168 TTCCCCGG 4.7 9.5e-04 -6.959 3.022 AT4G39838 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -337 -330 ATTCCGGC 6.8 2.1e-04 -8.468 3.678 AT4G39838 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -43 -36 ATAACCGC 5.0 8.0e-04 -7.131 3.097 AT4G39838 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -9 -2 CTTCTCGC 5.7 3.4e-04 -7.987 3.469 AT4G17550 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -368 -361 CTTCCCTC 5.2 5.9e-04 -7.435 3.229 RABG3F site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -101 -94 CCTCCCGC 6.2 2.9e-04 -8.146 3.538 AT3G18510 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -413 -406 TTACCTGC 5.2 5.9e-04 -7.435 3.229 AT3G18510 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -263 -256 ATTCCTGC 6.7 2.5e-04 -8.294 3.602 AT4G08425 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -349 -342 TTACCCTC 5.1 7.4e-04 -7.209 3.131 SAUR21 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -21 -14 TGTCCCAC 4.8 8.8e-04 -7.036 3.056 AT1G04787 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -472 -465 ACTTCCGC 4.7 9.5e-04 -6.959 3.022 AT1G04787 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -454 -447 TTTATCGC 4.7 9.5e-04 -6.959 3.022 AT1G04787 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -72 -65 TTTCCCCC 6.7 2.5e-04 -8.294 3.602 POLAR site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -40 -33 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 TPK2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -157 -150 TATCCAGC 5.3 5.1e-04 -7.581 3.292 AT3G13435 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -336 -329 GTTCACGC 5.6 3.5e-04 -7.958 3.456 AT2G33255 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -416 -409 TATCCCGA 5.3 5.1e-04 -7.581 3.292 AT2G33255 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -306 -299 ATTCCAGC 6.7 2.5e-04 -8.294 3.602 AT2G33255 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -249 -242 ATTCCCGA 6.7 2.5e-04 -8.294 3.602 LINC4 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -258 -251 ATACACGC 5.2 6.7e-04 -7.308 3.174 AT1G53340 site 5015_E2Fb_Athamap_20091028_ D -394 -387 TATCACGC 5.6 3.3e-04 -8.016 3.481 AT1G53340 site 5015_E2Fb_Athamap_20091028_ D -310 -303 ATTCCGGC 6.7 2.1e-04 -8.468 3.678 AT4G02489 site 5015_E2Fb_Athamap_20091028_ R -447 -440 TGTCCCGA 5.0 6.9e-04 -7.279 3.161 AT4G02489 site 5015_E2Fb_Athamap_20091028_ D -416 -409 GTTCCTGC 5.2 5.8e-04 -7.452 3.237 AT4G02489 site 5015_E2Fb_Athamap_20091028_ D -303 -296 TTAGCCGC 5.5 3.9e-04 -7.849 3.409 AT4G02489 site 5015_E2Fb_Athamap_20091028_ D -91 -84 TCTCTCGC 5.4 4.4e-04 -7.729 3.357 AT4G02489 site 5015_E2Fb_Athamap_20091028_ D -85 -78 GCTCCCGC 6.2 2.8e-04 -8.181 3.553 AT4G02489 site 5015_E2Fb_Athamap_20091028_ D -60 -53 ACTCTCGC 4.5 9.4e-04 -6.970 3.027 AT4G02110 site 5015_E2Fb_Athamap_20091028_ D -66 -59 TAGCCCGC 6.2 2.8e-04 -8.181 3.553 GLP9 site 5015_E2Fb_Athamap_20091028_ R -118 -111 GTTCCCTC 5.0 6.5e-04 -7.339 3.187 AT1G06190 site 5015_E2Fb_Athamap_20091028_ R -460 -453 TCTACCGC 5.5 3.6e-04 -7.929 3.444 AT1G06190 site 5015_E2Fb_Athamap_20091028_ R -175 -168 TTCCCCGG 4.7 8.2e-04 -7.106 3.086 AT4G39838 site 5015_E2Fb_Athamap_20091028_ D -337 -330 ATTCCGGC 6.7 2.1e-04 -8.468 3.678 AT4G39838 site 5015_E2Fb_Athamap_20091028_ R -43 -36 ATAACCGC 4.5 9.4e-04 -6.970 3.027 AT4G39838 site 5015_E2Fb_Athamap_20091028_ D -9 -2 CTTCTCGC 5.5 3.6e-04 -7.929 3.444 AT4G17550 site 5015_E2Fb_Athamap_20091028_ R -368 -361 CTTCCCTC 5.0 6.5e-04 -7.339 3.187 RABG3F site 5015_E2Fb_Athamap_20091028_ D -101 -94 CCTCCCGC 6.1 2.9e-04 -8.146 3.538 AT3G18510 site 5015_E2Fb_Athamap_20091028_ D -413 -406 TTACCTGC 5.1 5.8e-04 -7.452 3.237 AT3G18510 site 5015_E2Fb_Athamap_20091028_ R -263 -256 ATTCCTGC 6.6 2.5e-04 -8.294 3.602 AT4G08425 site 5015_E2Fb_Athamap_20091028_ R -349 -342 TTACCCTC 5.0 6.5e-04 -7.339 3.187 SAUR21 site 5015_E2Fb_Athamap_20091028_ D -21 -14 TGTCCCAC 4.7 7.9e-04 -7.143 3.102 AT1G04787 site 5015_E2Fb_Athamap_20091028_ R -454 -447 TTTATCGC 4.6 8.2e-04 -7.106 3.086 AT1G04787 site 5015_E2Fb_Athamap_20091028_ R -72 -65 TTTCCCCC 6.9 1.9e-04 -8.568 3.721 POLAR site 5015_E2Fb_Athamap_20091028_ D -40 -33 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 TPK2 site 5015_E2Fb_Athamap_20091028_ D -157 -150 TATCCAGC 5.3 4.4e-04 -7.729 3.357 AT3G13435 site 5015_E2Fb_Athamap_20091028_ R -336 -329 GTTCACGC 5.5 3.6e-04 -7.929 3.444 AT2G33255 site 5015_E2Fb_Athamap_20091028_ R -416 -409 TATCCCGA 5.3 4.4e-04 -7.729 3.357 AT2G33255 site 5015_E2Fb_Athamap_20091028_ R -306 -299 ATTCCAGC 6.6 2.4e-04 -8.335 3.620 AT2G33255 site 5015_E2Fb_Athamap_20091028_ D -249 -242 ATTCCCGA 6.6 2.4e-04 -8.335 3.620 LINC4 site 5015_E2Fb_Athamap_20091028_ D -258 -251 ATACACGC 4.7 7.9e-04 -7.143 3.102 AT4G02489 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -84 -74 CTCCCGCGCTC 7.1 1.2e-04 -9.028 3.921 AT4G02110 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -65 -55 AGCCCGCCATA 8.7 1.9e-05 -10.871 4.721 AT5G24040 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -500 -490 ATCGAGCTAAT 5.1 5.4e-04 -7.524 3.268 AT1G06190 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -31 -21 TTGCCGACAAA 5.1 5.4e-04 -7.524 3.268 AT4G39838 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -336 -326 TTCCGGCACAA 6.0 2.7e-04 -8.217 3.569 AT4G39838 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -251 -241 TTCTCACCATA 5.2 5.0e-04 -7.601 3.301 AT4G39838 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -47 -37 TAACCGCGAAA 7.0 1.2e-04 -9.028 3.921 AT4G17550 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -372 -362 TTCCCTCCATT 7.7 6.6e-05 -9.626 4.180 SAUR21 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -20 -10 GTCCCACGCTT 5.0 6.0e-04 -7.419 3.222 AT1G04787 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -76 -66 TTCCCCCCTAT 6.0 2.9e-04 -8.146 3.538 AT1G04787 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -75 -65 TTTCCCCCCTA 4.9 6.5e-04 -7.339 3.187 POLAR site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -39 -29 TTCCCTCCATA 8.3 3.1e-05 -10.382 4.509 TPK2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -74 -64 TTCAGGCCCAA 5.4 4.2e-04 -7.775 3.377 AT3G13435 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -392 -382 TTCTCGTCCAA 5.8 3.1e-04 -8.079 3.509 AT3G13435 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -340 -330 TTCACGCTAAG 5.6 3.9e-04 -7.849 3.409 AT3G13435 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -303 -293 TTGTCGCCCTT 5.1 5.4e-04 -7.524 3.268 AT2G33255 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -310 -300 TTCCAGCTGAA 4.7 8.3e-04 -7.094 3.081 AT2G33255 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -288 -278 CACCCACCAAA 4.5 9.1e-04 -7.002 3.041 ; ; 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_ 31 0 ; 2 5015_E2Fb_Athamap_20091028_ 30 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 18 0 ; TOTAL 79 0 ; Host name rsat ; Job started 2026-08-17.164215 ; Job done 2026-08-17.164216 ; Seconds 0.47 ; user 0.47 ; system 0.05 ; cuser 0.76 ; csystem 0.1