; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.110302_FjmOV0.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_2026-08-17.110302_Rxnp4e.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_2026-08-17.110302_Rxnp4e.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.110302_FjmOV0.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 AT5G03745|AT5G03745 limit START_END D -500 -1 . 0 0 0 0 AT5G12130|TERC limit START_END D -500 -1 . 0 0 0 0 AT2G04365|AT2G04365 limit START_END D -500 -1 . 0 0 0 0 AT1G42980|FH12 limit START_END D -500 -1 . 0 0 0 0 AT3G63540|AT3G63540 limit START_END D -26 -1 . 0 0 0 0 AT5G62690|TUBB3 limit START_END D -500 -1 . 0 0 0 0 AT4G20900|MS5 limit START_END D -500 -1 . 0 0 0 0 AT4G38932|AT4G38932 limit START_END D -500 -1 . 0 0 0 0 AT3G43870|AT3G43870 limit START_END D -500 -1 . 0 0 0 0 AT2G29100|ATGLR2.9 limit START_END D -500 -1 . 0 0 0 0 AT4G28380|AT4G28380 limit START_END D -500 -1 . 0 0 0 0 AT3G54670|SMC1 limit START_END D -500 -1 . 0 0 0 0 AT4G19680|IRT2 limit START_END D -500 -1 . 0 0 0 0 AT4G39500|CYP96A11 limit START_END D -500 -1 . 0 0 0 0 AT1G78670|GGH3 limit START_END D -500 -1 . 0 0 0 0 AT5G19970|AT5G19970 limit START_END D -500 -1 . 0 0 0 0 AT1G06103|AT1G06103 limit START_END D -500 -1 . 0 0 0 0 AT1G09794|AT1G09794 limit START_END D -500 -1 . 0 0 0 0 AT5G53210|SPCH limit START_END D -500 -1 . 0 0 0 0 AT1G75740|AT1G75740 limit START_END D -500 -1 . 0 0 0 0 AT3G51040|RTH limit START_END D -500 -1 . 0 0 0 0 AT3G49250|DMS3 limit START_END D -500 -1 . 0 0 0 0 AT1G52060|JAL9 limit START_END D -500 -1 . 0 0 0 0 AT2G04365|AT2G04365 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -400 -393 CTTCCCCC 4.9 8.0e-04 -7.131 3.097 AT2G04365|AT2G04365 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -98 -91 TTCCCCGA 4.8 8.8e-04 -7.036 3.056 AT2G04365|AT2G04365 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -77 -70 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 AT4G38932|AT4G38932 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -236 -229 TCTCTCGC 5.4 4.2e-04 -7.775 3.377 AT3G43870|AT3G43870 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -257 -250 TTTCCCGC 10.2 4.7e-06 -12.268 5.328 AT3G43870|AT3G43870 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -186 -179 ATGGCCGC 4.7 9.5e-04 -6.959 3.022 AT3G43870|AT3G43870 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -44 -37 TTTCCCGA 7.1 1.4e-04 -8.874 3.854 AT4G19680|IRT2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -57 -50 TTGCCGGC 5.1 7.4e-04 -7.209 3.131 AT1G78670|GGH3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -363 -356 ATCCACGC 4.8 9.5e-04 -6.959 3.022 AT1G78670|GGH3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -129 -122 ATGCCCGT 4.7 9.5e-04 -6.959 3.022 AT1G78670|GGH3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -37 -30 ACTCGCGC 5.2 5.9e-04 -7.435 3.229 AT1G09794|AT1G09794 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -202 -195 TTTCACGC 7.4 6.6e-05 -9.626 4.180 AT5G53210|SPCH site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -364 -357 TTTAGCGC 4.8 8.8e-04 -7.036 3.056 AT5G53210|SPCH site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -146 -139 TTACCCCC 4.8 8.8e-04 -7.036 3.056 AT3G49250|DMS3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -468 -461 ATTCCAGC 6.7 2.5e-04 -8.294 3.602 AT2G04365|AT2G04365 site 5015_E2Fb_Athamap_20091028_ R -400 -393 CTTCCCCC 4.8 7.9e-04 -7.143 3.102 AT2G04365|AT2G04365 site 5015_E2Fb_Athamap_20091028_ R -98 -91 TTCCCCGA 4.8 7.9e-04 -7.143 3.102 AT2G04365|AT2G04365 site 5015_E2Fb_Athamap_20091028_ R -77 -70 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 AT4G38932|AT4G38932 site 5015_E2Fb_Athamap_20091028_ R -236 -229 TCTCTCGC 5.4 4.4e-04 -7.729 3.357 AT3G43870|AT3G43870 site 5015_E2Fb_Athamap_20091028_ D -257 -250 TTTCCCGC 10.7 4.7e-06 -12.268 5.328 AT3G43870|AT3G43870 site 5015_E2Fb_Athamap_20091028_ D -44 -37 TTTCCCGA 7.3 1.3e-04 -8.948 3.886 AT4G19680|IRT2 site 5015_E2Fb_Athamap_20091028_ R -57 -50 TTGCCGGC 5.0 6.5e-04 -7.339 3.187 AT1G78670|GGH3 site 5015_E2Fb_Athamap_20091028_ R -403 -396 TCTCCCCC 4.6 8.2e-04 -7.106 3.086 AT1G78670|GGH3 site 5015_E2Fb_Athamap_20091028_ R -37 -30 ACTCGCGC 4.8 7.5e-04 -7.195 3.125 AT1G09794|AT1G09794 site 5015_E2Fb_Athamap_20091028_ D -202 -195 TTTCACGC 7.6 5.8e-05 -9.755 4.237 AT5G53210|SPCH site 5015_E2Fb_Athamap_20091028_ R -364 -357 TTTAGCGC 4.7 7.9e-04 -7.143 3.102 AT5G53210|SPCH site 5015_E2Fb_Athamap_20091028_ D -146 -139 TTACCCCC 4.7 7.9e-04 -7.143 3.102 AT3G49250|DMS3 site 5015_E2Fb_Athamap_20091028_ R -468 -461 ATTCCAGC 6.6 2.4e-04 -8.335 3.620 AT5G12130|TERC site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -229 -219 TTCTCGACAAT 5.3 4.6e-04 -7.684 3.337 AT5G12130|TERC site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -118 -108 ATCTCGCCAAT 7.8 5.3e-05 -9.845 4.276 AT2G04365|AT2G04365 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -404 -394 TTCCCCCCTTA 5.7 3.3e-04 -8.016 3.481 AT2G04365|AT2G04365 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -298 -288 GTCCAGCCAAT 5.8 3.1e-04 -8.079 3.509 AT2G04365|AT2G04365 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -102 -92 TCCCCGACCTT 5.8 3.3e-04 -8.016 3.481 AT5G62690|TUBB3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -322 -312 TTTCCTCCAAT 4.5 9.1e-04 -7.002 3.041 AT4G38932|AT4G38932 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -240 -230 CTCTCGCCGAT 4.5 9.1e-04 -7.002 3.041 AT3G43870|AT3G43870 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -256 -246 TTCCCGCTGAA 8.3 3.1e-05 -10.382 4.509 AT3G43870|AT3G43870 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -230 -220 CTCACGCCACA 4.4 9.8e-04 -6.928 3.009 AT1G78670|GGH3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -405 -395 TTCTCCCCCAT 5.1 5.4e-04 -7.524 3.268 AT1G09794|AT1G09794 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -415 -405 TGCTCGCTCTA 5.6 3.6e-04 -7.929 3.444 AT5G53210|SPCH site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -146 -136 TTACCCCCATA 5.0 6.0e-04 -7.419 3.222 AT1G75740|AT1G75740 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -220 -210 AACCCACTCAT 4.7 8.3e-04 -7.094 3.081 ; ; 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 11026 ; N residues 0 ; Matches per matrix ; matrix name matches scored ; 1 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ 15 0 ; 2 5015_E2Fb_Athamap_20091028_ 13 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 13 0 ; TOTAL 41 0 ; Host name rsat ; Job started 2026-08-17.110302 ; Job done 2026-08-17.110303 ; Seconds 0.45 ; user 0.45 ; system 0.05 ; cuser 0.82 ; csystem 0.07