; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.115726_eYwIQ2.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_2026-08-17.115726_enVXbo.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_2026-08-17.115726_enVXbo.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.115726_eYwIQ2.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 AT4G13360 limit START_END D -500 -1 . 0 0 0 0 PAPS3 limit START_END D -500 -1 . 0 0 0 0 AT1G32600 limit START_END D -500 -1 . 0 0 0 0 AT3G02890 limit START_END D -500 -1 . 0 0 0 0 AT1G11572 limit START_END D -500 -1 . 0 0 0 0 AT5G55135 limit START_END D -500 -1 . 0 0 0 0 ATY53 limit START_END D -500 -1 . 0 0 0 0 AT2G39445 limit START_END D -500 -1 . 0 0 0 0 MFP1 limit START_END D -500 -1 . 0 0 0 0 AT2G04295 limit START_END D -500 -1 . 0 0 0 0 GATA27 limit START_END D -500 -1 . 0 0 0 0 AT3G20450 limit START_END D -500 -1 . 0 0 0 0 AT3G09015 limit START_END D -500 -1 . 0 0 0 0 PERK7 limit START_END D -500 -1 . 0 0 0 0 AT3G46190 limit START_END D -500 -1 . 0 0 0 0 AT1G09575 limit START_END D -500 -1 . 0 0 0 0 AT1G49900 limit START_END D -500 -1 . 0 0 0 0 TGD4 limit START_END D -500 -1 . 0 0 0 0 AT2G10537 limit START_END D -500 -1 . 0 0 0 0 SKIP22 limit START_END D -500 -1 . 0 0 0 0 CYP704A2 limit START_END D -500 -1 . 0 0 0 0 AT4G05965 limit START_END D -500 -1 . 0 0 0 0 CLE10 limit START_END D -500 -1 . 0 0 0 0 CDA6 limit START_END D -500 -1 . 0 0 0 0 AT1G32600 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -100 -93 AATCACGC 4.8 9.5e-04 -6.959 3.022 AT1G32600 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -46 -39 TTTCCCGG 7.0 1.6e-04 -8.740 3.796 AT3G02890 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -317 -310 GTTCCCAC 5.1 6.7e-04 -7.308 3.174 AT3G02890 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -138 -131 TTTACCGC 7.6 4.7e-05 -9.965 4.328 MFP1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -405 -398 TCTCCCTC 4.9 8.0e-04 -7.131 3.097 MFP1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -15 -8 TTGCCCTC 4.8 8.8e-04 -7.036 3.056 AT2G04295 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -87 -80 TACCCCGC 6.1 2.9e-04 -8.146 3.538 PERK7 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -470 -463 ATTCTCGC 7.1 1.4e-04 -8.874 3.854 PERK7 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -439 -432 TTACCCGT 5.3 5.1e-04 -7.581 3.292 PERK7 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -183 -176 CCTCCCGC 6.2 2.9e-04 -8.146 3.538 AT1G49900 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -417 -410 TGTCCCAC 4.8 8.8e-04 -7.036 3.056 AT1G49900 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -231 -224 TATCCCGG 5.3 5.9e-04 -7.435 3.229 TGD4 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -271 -264 ATAACCGC 5.0 8.0e-04 -7.131 3.097 TGD4 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -56 -49 CTTCCCGT 5.4 4.2e-04 -7.775 3.377 SKIP22 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -480 -473 TTGGCCGC 5.1 7.4e-04 -7.209 3.131 CYP704A2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -301 -294 TTTCACGC 7.4 6.6e-05 -9.626 4.180 AT4G05965 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -359 -352 CTTCCCGT 5.4 4.2e-04 -7.775 3.377 CDA6 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -381 -374 TTACCCTC 5.1 7.4e-04 -7.209 3.131 AT1G32600 site 5015_E2Fb_Athamap_20091028_ D -46 -39 TTTCCCGG 7.2 1.4e-04 -8.874 3.854 AT3G02890 site 5015_E2Fb_Athamap_20091028_ R -317 -310 GTTCCCAC 5.0 6.9e-04 -7.279 3.161 AT3G02890 site 5015_E2Fb_Athamap_20091028_ R -138 -131 TTTACCGC 7.8 3.7e-05 -10.205 4.432 MFP1 site 5015_E2Fb_Athamap_20091028_ R -405 -398 TCTCCCTC 4.8 7.5e-04 -7.195 3.125 MFP1 site 5015_E2Fb_Athamap_20091028_ D -15 -8 TTGCCCTC 4.7 7.9e-04 -7.143 3.102 AT2G04295 site 5015_E2Fb_Athamap_20091028_ D -87 -80 TACCCCGC 6.0 2.9e-04 -8.146 3.538 PERK7 site 5015_E2Fb_Athamap_20091028_ R -470 -463 ATTCTCGC 6.9 1.9e-04 -8.568 3.721 PERK7 site 5015_E2Fb_Athamap_20091028_ R -439 -432 TTACCCGT 5.2 5.1e-04 -7.581 3.292 PERK7 site 5015_E2Fb_Athamap_20091028_ R -183 -176 CCTCCCGC 6.1 2.9e-04 -8.146 3.538 AT1G49900 site 5015_E2Fb_Athamap_20091028_ D -417 -410 TGTCCCAC 4.7 7.9e-04 -7.143 3.102 AT1G49900 site 5015_E2Fb_Athamap_20091028_ D -231 -224 TATCCCGG 5.2 5.1e-04 -7.581 3.292 TGD4 site 5015_E2Fb_Athamap_20091028_ R -271 -264 ATAACCGC 4.5 9.4e-04 -6.970 3.027 TGD4 site 5015_E2Fb_Athamap_20091028_ R -56 -49 CTTCCCGT 5.3 5.1e-04 -7.581 3.292 SKIP22 site 5015_E2Fb_Athamap_20091028_ D -480 -473 TTGGCCGC 5.0 6.5e-04 -7.339 3.187 CYP704A2 site 5015_E2Fb_Athamap_20091028_ D -301 -294 TTTCACGC 7.6 5.8e-05 -9.755 4.237 AT4G05965 site 5015_E2Fb_Athamap_20091028_ D -359 -352 CTTCCCGT 5.3 5.1e-04 -7.581 3.292 CDA6 site 5015_E2Fb_Athamap_20091028_ R -477 -470 TTCCCCAC 4.5 9.4e-04 -6.970 3.027 CDA6 site 5015_E2Fb_Athamap_20091028_ R -381 -374 TTACCCTC 5.0 6.5e-04 -7.339 3.187 PAPS3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -42 -32 ATCCAGCGCAG 5.1 5.4e-04 -7.524 3.268 AT1G32600 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -99 -89 ATCACGCTCTC 4.4 9.8e-04 -6.928 3.009 AT1G32600 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -45 -35 TTCCCGGACAA 5.8 3.1e-04 -8.079 3.509 AT3G02890 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -446 -436 TTTCAGCCCAA 5.2 5.4e-04 -7.524 3.268 AT3G02890 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -321 -311 TTCCCACTTAT 4.5 9.1e-04 -7.002 3.041 AT3G02890 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -142 -132 TTACCGCCATG 6.5 1.9e-04 -8.568 3.721 AT2G04295 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -207 -197 AACCAGCTCAT 4.9 7.2e-04 -7.236 3.143 AT1G49900 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -231 -221 ATCCCGGGATA 6.5 1.8e-04 -8.623 3.745 AT1G49900 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -230 -220 ATCCCGGGATT 5.8 3.1e-04 -8.079 3.509 TGD4 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -60 -50 TTCCCGTTTAA 4.8 7.7e-04 -7.169 3.114 SKIP22 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -481 -471 TTGCGGCCAAA 5.1 6.0e-04 -7.419 3.222 SKIP22 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -58 -48 ATACGGCCCAT 4.6 8.3e-04 -7.094 3.081 CYP704A2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -232 -222 ATCCAGCGAAT 6.6 1.6e-04 -8.740 3.796 AT4G05965 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -358 -348 TTCCCGTTTAT 4.6 8.3e-04 -7.094 3.081 CDA6 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -480 -470 TTCCCCACCTT 4.4 9.8e-04 -6.928 3.009 ; ; 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_ 18 0 ; 2 5015_E2Fb_Athamap_20091028_ 18 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 15 0 ; TOTAL 51 0 ; Host name rsat ; Job started 2026-08-17.115726 ; Job done 2026-08-17.115727 ; Seconds 0.47 ; user 0.47 ; system 0.05 ; cuser 0.8 ; csystem 0.09