; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.133406_dFsfqB.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_2026-08-17.133406_djkArW.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_2026-08-17.133406_djkArW.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.133406_dFsfqB.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 BHLH28 limit START_END D -500 -1 . 0 0 0 0 AT1G75600 limit START_END D -500 -1 . 0 0 0 0 AT5G07225 limit START_END D -500 -1 . 0 0 0 0 AT1G09313 limit START_END D -500 -1 . 0 0 0 0 AT5G50805 limit START_END D -500 -1 . 0 0 0 0 AT1G56020 limit START_END D -500 -1 . 0 0 0 0 AT3G25440 limit START_END D -500 -1 . 0 0 0 0 IQD23 limit START_END D -500 -1 . 0 0 0 0 AT3G48131 limit START_END D -500 -1 . 0 0 0 0 SUC1 limit START_END D -500 -1 . 0 0 0 0 LEP limit START_END D -500 -1 . 0 0 0 0 PAT23 limit START_END D -500 -1 . 0 0 0 0 AT2G17300 limit START_END D -500 -1 . 0 0 0 0 AT3G25930 limit START_END D -500 -1 . 0 0 0 0 AGL91 limit START_END D -500 -1 . 0 0 0 0 EXPA7 limit START_END D -500 -1 . 0 0 0 0 AT5G17080 limit START_END D -500 -1 . 0 0 0 0 AT1G57440 limit START_END D -500 -1 . 0 0 0 0 AT5G01045 limit START_END D -500 -1 . 0 0 0 0 HGL1 limit START_END D -500 -1 . 0 0 0 0 PXL1 limit START_END D -500 -1 . 0 0 0 0 RPL11A limit START_END D -500 -1 . 0 0 0 0 AT1G67760 limit START_END D -500 -1 . 0 0 0 0 AT2G16019 limit START_END D -500 -1 . 0 0 0 0 BHLH28 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -419 -412 ATTGCCGC 7.0 1.6e-04 -8.740 3.796 BHLH28 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -132 -125 TTTCCCGA 7.1 1.4e-04 -8.874 3.854 AT1G75600 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -92 -85 TCTCCCGT 5.2 6.7e-04 -7.308 3.174 AT5G07225 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -326 -319 GTTCCCAC 5.1 6.7e-04 -7.308 3.174 AT5G07225 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -170 -163 TTTCTCGC 7.4 6.6e-05 -9.626 4.180 AT1G56020 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -292 -285 CTTGCCGC 5.6 3.5e-04 -7.958 3.456 AT3G25440 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -492 -485 TTGACCGC 5.1 6.7e-04 -7.308 3.174 AT3G48131 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -491 -484 GTTCCCTC 5.2 6.7e-04 -7.308 3.174 AT3G48131 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -233 -226 TTCCTCGC 5.2 5.9e-04 -7.435 3.229 AT3G48131 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -110 -103 TATCCCTC 5.2 5.9e-04 -7.435 3.229 SUC1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -64 -57 ATTCCCGT 6.8 2.1e-04 -8.468 3.678 AT3G25930 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -427 -420 TCTCCCGA 5.1 6.7e-04 -7.308 3.174 AT3G25930 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -358 -351 TATCCAGC 5.3 5.1e-04 -7.581 3.292 AT3G25930 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -213 -206 ATACACGC 5.2 6.7e-04 -7.308 3.174 AT3G25930 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -208 -201 TATCCGGC 5.5 4.2e-04 -7.775 3.377 AT5G17080 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -483 -476 TTACCTGC 5.2 5.9e-04 -7.435 3.229 AT5G17080 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -289 -282 TTCCCAGC 4.8 8.8e-04 -7.036 3.056 AT5G17080 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -67 -60 CTTCCTGC 5.3 5.1e-04 -7.581 3.292 AT1G57440 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -240 -233 TTTCCCAC 6.9 2.1e-04 -8.468 3.678 PXL1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -315 -308 TGTCCCAC 4.8 8.8e-04 -7.036 3.056 AT2G16019 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -53 -46 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 AT2G16019 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -18 -11 CTTCTCGC 5.7 3.4e-04 -7.987 3.469 BHLH28 site 5015_E2Fb_Athamap_20091028_ R -419 -412 ATTGCCGC 6.8 1.9e-04 -8.568 3.721 BHLH28 site 5015_E2Fb_Athamap_20091028_ D -132 -125 TTTCCCGA 7.3 1.3e-04 -8.948 3.886 AT1G75600 site 5015_E2Fb_Athamap_20091028_ D -92 -85 TCTCCCGT 5.1 5.8e-04 -7.452 3.237 AT5G07225 site 5015_E2Fb_Athamap_20091028_ D -326 -319 GTTCCCAC 5.0 6.9e-04 -7.279 3.161 AT5G07225 site 5015_E2Fb_Athamap_20091028_ D -170 -163 TTTCTCGC 7.6 5.8e-05 -9.755 4.237 AT1G56020 site 5015_E2Fb_Athamap_20091028_ D -292 -285 CTTGCCGC 5.4 3.9e-04 -7.849 3.409 AT3G25440 site 5015_E2Fb_Athamap_20091028_ R -492 -485 TTGACCGC 5.1 6.5e-04 -7.339 3.187 AT3G48131 site 5015_E2Fb_Athamap_20091028_ R -491 -484 GTTCCCTC 5.0 6.5e-04 -7.339 3.187 AT3G48131 site 5015_E2Fb_Athamap_20091028_ R -233 -226 TTCCTCGC 5.1 5.8e-04 -7.452 3.237 AT3G48131 site 5015_E2Fb_Athamap_20091028_ D -110 -103 TATCCCTC 5.1 5.8e-04 -7.452 3.237 SUC1 site 5015_E2Fb_Athamap_20091028_ D -64 -57 ATTCCCGT 6.6 2.4e-04 -8.335 3.620 AT3G25930 site 5015_E2Fb_Athamap_20091028_ R -427 -420 TCTCCCGA 5.0 6.5e-04 -7.339 3.187 AT3G25930 site 5015_E2Fb_Athamap_20091028_ R -358 -351 TATCCAGC 5.3 4.4e-04 -7.729 3.357 AT3G25930 site 5015_E2Fb_Athamap_20091028_ R -213 -206 ATACACGC 4.7 7.9e-04 -7.143 3.102 AT3G25930 site 5015_E2Fb_Athamap_20091028_ D -208 -201 TATCCGGC 5.4 3.9e-04 -7.849 3.409 AT5G17080 site 5015_E2Fb_Athamap_20091028_ D -483 -476 TTACCTGC 5.1 5.8e-04 -7.452 3.237 AT5G17080 site 5015_E2Fb_Athamap_20091028_ R -289 -282 TTCCCAGC 4.8 7.9e-04 -7.143 3.102 AT5G17080 site 5015_E2Fb_Athamap_20091028_ D -67 -60 CTTCCTGC 5.2 5.1e-04 -7.581 3.292 AT1G57440 site 5015_E2Fb_Athamap_20091028_ R -240 -233 TTTCCCAC 7.1 1.7e-04 -8.680 3.770 PXL1 site 5015_E2Fb_Athamap_20091028_ D -315 -308 TGTCCCAC 4.7 7.9e-04 -7.143 3.102 AT2G16019 site 5015_E2Fb_Athamap_20091028_ R -53 -46 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 AT2G16019 site 5015_E2Fb_Athamap_20091028_ R -18 -11 CTTCTCGC 5.5 3.6e-04 -7.929 3.444 BHLH28 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -423 -413 TTGCCGCCGCA 4.6 9.1e-04 -7.002 3.041 BHLH28 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -131 -121 TTCCCGACATA 8.7 2.1e-05 -10.771 4.678 AT1G75600 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -91 -81 CTCCCGTTAAT 4.5 9.1e-04 -7.002 3.041 AT1G75600 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -70 -60 TAACCGACCTA 4.7 7.7e-04 -7.169 3.114 AT5G07225 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -410 -400 TTACCGTCAAA 5.4 4.6e-04 -7.684 3.337 AT5G07225 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -325 -315 TTCCCACCACT 5.8 3.1e-04 -8.079 3.509 AT5G07225 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -169 -159 TTCTCGCTTAT 5.3 4.6e-04 -7.684 3.337 AT1G09313 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -196 -186 TTCGGGCCCTT 7.0 1.3e-04 -8.948 3.886 AT5G50805 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -426 -416 TTGCAGCCATT 4.5 9.8e-04 -6.928 3.009 AT1G56020 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -291 -281 TTGCCGCTAAG 5.3 4.6e-04 -7.684 3.337 AT3G25440 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -373 -363 ATTCCGCCAAG 5.4 4.6e-04 -7.684 3.337 AT3G48131 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -495 -485 TTCCCTCAATT 4.6 8.3e-04 -7.094 3.081 AT3G48131 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -434 -424 CTTCCGCCATT 5.6 3.9e-04 -7.849 3.409 AT3G48131 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -410 -400 AACGCTCCAAA 5.1 5.4e-04 -7.524 3.268 AT3G48131 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -109 -99 ATCCCTCACAA 4.7 7.7e-04 -7.169 3.114 SUC1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -63 -53 TTCCCGTAAAA 5.7 3.6e-04 -7.929 3.444 AT3G25930 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -362 -352 ATCCAGCCCAT 7.6 6.6e-05 -9.626 4.180 AT3G25930 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -217 -207 TACACGCCATT 7.6 6.6e-05 -9.626 4.180 AGL91 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -387 -377 TTTCCACCCAA 4.9 6.5e-04 -7.339 3.187 EXPA7 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -38 -28 TCCCCTCTATA 4.6 8.3e-04 -7.094 3.081 AT1G57440 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -244 -234 TTCCCACTCAT 6.9 1.3e-04 -8.948 3.886 PXL1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -241 -231 AACCCACGATT 4.7 7.7e-04 -7.169 3.114 AT2G16019 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -22 -12 TTCTCGCCGAC 4.9 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 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_ 22 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 23 0 ; TOTAL 67 0 ; Host name rsat ; Job started 2026-08-17.133406 ; Job done 2026-08-17.133407 ; Seconds 0.43 ; user 0.43 ; system 0.05 ; cuser 0.8 ; csystem 0.11