; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.105853_KzxGFm.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_2026-08-17.105853_EQU30H.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.105853_EQU30H.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_2026-08-17.105853_KzxGFm.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 AT3G19570|SCO3 limit START_END D -500 -1 . 0 0 0 0 AT5G41560|AT5G41560 limit START_END D -500 -1 . 0 0 0 0 AT5G15740|OFUT34 limit START_END D -500 -1 . 0 0 0 0 AT5G04710|AT5G04710 limit START_END D -500 -1 . 0 0 0 0 AT5G02275|AT5G02275 limit START_END D -500 -1 . 0 0 0 0 AT2G02500|ISPD limit START_END D -500 -1 . 0 0 0 0 AT5G56960|AT5G56960 limit START_END D -500 -1 . 0 0 0 0 ATMG00270|NAD6 limit START_END D -500 -1 . 0 0 0 0 AT3G29580|AT3G29580 limit START_END D -500 -1 . 0 0 0 0 AT2G34610|AT2G34610 limit START_END D -500 -1 . 0 0 0 0 AT2G08375|AT2G08375 limit START_END D -500 -1 . 0 0 0 0 AT2G25297|AT2G25297 limit START_END D -500 -1 . 0 0 0 0 AT4G11920|FZR1 limit START_END D -500 -1 . 0 0 0 0 AT4G25260|PMEI7 limit START_END D -500 -1 . 0 0 0 0 AT1G66783|MIR157A limit START_END D -500 -1 . 0 0 0 0 AT4G31265|AT4G31265 limit START_END D -500 -1 . 0 0 0 0 AT1G51310|AT1G51310 limit START_END D -500 -1 . 0 0 0 0 AT3G61060|AtPP2-A13 limit START_END D -500 -1 . 0 0 0 0 AT5G60170|AT5G60170 limit START_END D -500 -1 . 0 0 0 0 AT2G35387|AT2G35387 limit START_END D -500 -1 . 0 0 0 0 AT4G26675|AT4G26675 limit START_END D -500 -1 . 0 0 0 0 AT4G20470|AT4G20470 limit START_END D -500 -1 . 0 0 0 0 AT1G08695|SCRL3 limit START_END D -500 -1 . 0 0 0 0 AT5G15740|OFUT34 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -215 -208 TATCCCTC 5.2 5.9e-04 -7.435 3.229 AT5G04710|AT5G04710 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -496 -489 TTCGCCGC 5.4 4.2e-04 -7.775 3.377 AT2G02500|ISPD site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -50 -43 TTTCCGGC 7.2 1.0e-04 -9.210 4.000 AT5G56960|AT5G56960 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -386 -379 AATCCCGC 7.6 4.7e-05 -9.965 4.328 ATMG00270|NAD6 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -425 -418 ATTCACGC 7.0 1.6e-04 -8.740 3.796 ATMG00270|NAD6 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -419 -412 GTACCCGC 6.6 2.6e-04 -8.255 3.585 ATMG00270|NAD6 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -209 -202 TCTACCGC 5.6 3.5e-04 -7.958 3.456 AT2G34610|AT2G34610 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -342 -335 AGTACCGC 5.1 6.7e-04 -7.308 3.174 AT2G08375|AT2G08375 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -199 -192 ATACCCGC 8.0 2.8e-05 -10.483 4.553 AT2G08375|AT2G08375 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -29 -22 ATTCCCGG 6.6 2.6e-04 -8.255 3.585 AT2G08375|AT2G08375 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -28 -21 TTCCCGGC 4.9 8.0e-04 -7.131 3.097 AT2G25297|AT2G25297 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -207 -200 TCTCCGGC 5.2 5.9e-04 -7.435 3.229 AT4G25260|PMEI7 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -339 -332 TATCCCGT 5.4 4.2e-04 -7.775 3.377 AT4G25260|PMEI7 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -310 -303 ATACACGC 5.2 6.7e-04 -7.308 3.174 AT1G66783|MIR157A site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -158 -151 ATACTCGC 5.2 5.9e-04 -7.435 3.229 AT4G31265|AT4G31265 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -457 -450 GTTCTCGC 5.7 3.4e-04 -7.987 3.469 AT4G31265|AT4G31265 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -104 -97 TTACCAGC 5.2 5.9e-04 -7.435 3.229 AT1G51310|AT1G51310 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -254 -247 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 AT3G61060|AtPP2-A13 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -352 -345 ATCACCGC 4.8 9.5e-04 -6.959 3.022 AT2G35387|AT2G35387 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -254 -247 TGTTCCGC 5.1 6.7e-04 -7.308 3.174 AT4G26675|AT4G26675 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -232 -225 TTGCACGC 5.3 5.9e-04 -7.435 3.229 AT4G26675|AT4G26675 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -137 -130 TTTGCCGC 7.3 7.6e-05 -9.485 4.119 AT5G15740|OFUT34 site 5015_E2Fb_Athamap_20091028_ D -215 -208 TATCCCTC 5.1 5.8e-04 -7.452 3.237 AT5G04710|AT5G04710 site 5015_E2Fb_Athamap_20091028_ D -496 -489 TTCGCCGC 5.4 4.4e-04 -7.729 3.357 AT2G02500|ISPD site 5015_E2Fb_Athamap_20091028_ R -50 -43 TTTCCGGC 7.4 9.3e-05 -9.283 4.032 AT5G56960|AT5G56960 site 5015_E2Fb_Athamap_20091028_ D -386 -379 AATCCCGC 7.4 9.3e-05 -9.283 4.032 ATMG00270|NAD6 site 5015_E2Fb_Athamap_20091028_ D -425 -418 ATTCACGC 6.9 1.9e-04 -8.568 3.721 ATMG00270|NAD6 site 5015_E2Fb_Athamap_20091028_ R -419 -412 GTACCCGC 6.4 2.6e-04 -8.255 3.585 ATMG00270|NAD6 site 5015_E2Fb_Athamap_20091028_ D -209 -202 TCTACCGC 5.5 3.6e-04 -7.929 3.444 AT2G34610|AT2G34610 site 5015_E2Fb_Athamap_20091028_ R -342 -335 AGTACCGC 4.7 7.9e-04 -7.143 3.102 AT2G08375|AT2G08375 site 5015_E2Fb_Athamap_20091028_ D -199 -192 ATACCCGC 7.8 3.7e-05 -10.205 4.432 AT2G08375|AT2G08375 site 5015_E2Fb_Athamap_20091028_ D -29 -22 ATTCCCGG 6.5 2.5e-04 -8.294 3.602 AT2G08375|AT2G08375 site 5015_E2Fb_Athamap_20091028_ D -28 -21 TTCCCGGC 4.9 7.5e-04 -7.195 3.125 AT2G25297|AT2G25297 site 5015_E2Fb_Athamap_20091028_ R -207 -200 TCTCCGGC 5.1 5.8e-04 -7.452 3.237 AT4G25260|PMEI7 site 5015_E2Fb_Athamap_20091028_ R -339 -332 TATCCCGT 5.4 4.4e-04 -7.729 3.357 AT4G25260|PMEI7 site 5015_E2Fb_Athamap_20091028_ R -310 -303 ATACACGC 4.7 7.9e-04 -7.143 3.102 AT1G66783|MIR157A site 5015_E2Fb_Athamap_20091028_ R -158 -151 ATACTCGC 4.8 7.5e-04 -7.195 3.125 AT4G31265|AT4G31265 site 5015_E2Fb_Athamap_20091028_ R -457 -450 GTTCTCGC 5.5 3.6e-04 -7.929 3.444 AT4G31265|AT4G31265 site 5015_E2Fb_Athamap_20091028_ R -104 -97 TTACCAGC 5.1 5.8e-04 -7.452 3.237 AT1G51310|AT1G51310 site 5015_E2Fb_Athamap_20091028_ R -254 -247 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 AT2G35387|AT2G35387 site 5015_E2Fb_Athamap_20091028_ D -254 -247 TGTTCCGC 5.1 6.5e-04 -7.339 3.187 AT4G26675|AT4G26675 site 5015_E2Fb_Athamap_20091028_ D -232 -225 TTGCACGC 5.2 5.1e-04 -7.581 3.292 AT4G26675|AT4G26675 site 5015_E2Fb_Athamap_20091028_ R -158 -151 TTCCCCTC 4.6 8.2e-04 -7.106 3.086 AT4G26675|AT4G26675 site 5015_E2Fb_Athamap_20091028_ R -137 -130 TTTGCCGC 7.5 6.2e-05 -9.688 4.208 AT3G19570|SCO3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -476 -466 AACCCACCATT 5.3 4.6e-04 -7.684 3.337 AT5G15740|OFUT34 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -278 -268 AACCTGCTAAT 4.7 7.7e-04 -7.169 3.114 AT5G02275|AT5G02275 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -252 -242 AACACGCCTAT 4.6 8.3e-04 -7.094 3.081 AT2G02500|ISPD site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -220 -210 AACCCGCTCCA 6.4 2.1e-04 -8.468 3.678 AT2G02500|ISPD site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -54 -44 TTCCGGCGAAG 5.7 3.3e-04 -8.016 3.481 AT5G56960|AT5G56960 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -385 -375 ATCCCGCGACG 6.3 2.1e-04 -8.468 3.678 ATMG00270|NAD6 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -423 -413 TACCCGCGTGA 6.2 2.3e-04 -8.377 3.638 ATMG00270|NAD6 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -358 -348 ATCGCGCAGTA 5.2 5.0e-04 -7.601 3.301 AT3G29580|AT3G29580 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -119 -109 TTGCGGCCCAA 5.4 4.2e-04 -7.775 3.377 AT2G08375|AT2G08375 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -198 -188 TACCCGCTAAG 7.9 4.8e-05 -9.944 4.319 AT2G25297|AT2G25297 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -211 -201 CTCCGGCCAAA 6.1 2.7e-04 -8.217 3.569 AT4G11920|FZR1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -70 -60 TTCAAGCCCAA 5.4 4.2e-04 -7.775 3.377 AT1G66783|MIR157A site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -328 -318 TCTCCGCTCAA 5.1 5.4e-04 -7.524 3.268 AT1G66783|MIR157A site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -162 -152 TACTCGCCAGT 5.9 3.1e-04 -8.079 3.509 AT4G31265|AT4G31265 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -365 -355 TTGCCTCCAAA 4.8 7.2e-04 -7.236 3.143 AT4G31265|AT4G31265 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -310 -300 TTCAAGCCCAT 5.2 5.0e-04 -7.601 3.301 AT1G51310|AT1G51310 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -258 -248 TTCCCTCAAAT 5.0 6.0e-04 -7.419 3.222 AT4G26675|AT4G26675 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -141 -131 TTGCCGCTGAA 4.9 6.5e-04 -7.339 3.187 AT1G08695|SCRL3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -486 -476 TGCCTGCCCTT 5.7 3.3e-04 -8.016 3.481 ; ; 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 23 ; Sum of sequence lengths 11500 ; 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_ 19 0 ; TOTAL 63 0 ; Host name rsat ; Job started 2026-08-17.105853 ; Job done 2026-08-17.105854 ; Seconds 0.46 ; user 0.46 ; system 0.04 ; cuser 0.83 ; csystem 0.08