; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.163145_L0npgO.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_2026-08-17.163145_9b5KJA.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.163145_9b5KJA.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_2026-08-17.163145_L0npgO.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 AT5G66510 limit START_END D -500 -1 . 0 0 0 0 AT5G48835 limit START_END D -500 -1 . 0 0 0 0 AT1G04083 limit START_END D -500 -1 . 0 0 0 0 LACS4 limit START_END D -500 -1 . 0 0 0 0 SCPL50 limit START_END D -500 -1 . 0 0 0 0 DRP3A limit START_END D -500 -1 . 0 0 0 0 RGTA2 limit START_END D -500 -1 . 0 0 0 0 AT1G08683 limit START_END D -500 -1 . 0 0 0 0 AT1G70860 limit START_END D -500 -1 . 0 0 0 0 AT1G75210 limit START_END D -500 -1 . 0 0 0 0 AT2G02060 limit START_END D -500 -1 . 0 0 0 0 AT1G09487 limit START_END D -500 -1 . 0 0 0 0 RPL32B limit START_END D -500 -1 . 0 0 0 0 ECT7 limit START_END D -500 -1 . 0 0 0 0 BOLA1 limit START_END D -500 -1 . 0 0 0 0 EARLI1 limit START_END D -500 -1 . 0 0 0 0 AT4G31320 limit START_END D -500 -1 . 0 0 0 0 TTG1 limit START_END D -500 -1 . 0 0 0 0 SCPL45 limit START_END D -500 -1 . 0 0 0 0 BAD1 limit START_END D -500 -1 . 0 0 0 0 AT1G09170 limit START_END D -500 -1 . 0 0 0 0 AT1G30540 limit START_END D -500 -1 . 0 0 0 0 AT1G56740 limit START_END D -500 -1 . 0 0 0 0 NFYC2 limit START_END D -500 -1 . 0 0 0 0 AT3G62790 limit START_END D -500 -1 . 0 0 0 0 AT3G03285 limit START_END D -500 -1 . 0 0 0 0 LCR33 limit START_END D -500 -1 . 0 0 0 0 AT1G20132 limit START_END D -500 -1 . 0 0 0 0 AT5G66510 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -346 -339 ATCCACGC 4.8 9.5e-04 -6.959 3.022 AT5G48835 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -216 -209 AATCACGC 4.8 9.5e-04 -6.959 3.022 LACS4 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -499 -492 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 LACS4 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -195 -188 TATCCCCC 4.9 8.0e-04 -7.131 3.097 DRP3A site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -499 -492 TGTCCCTC 4.9 8.8e-04 -7.036 3.056 AT1G08683 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -145 -138 ATTCACGC 7.0 1.6e-04 -8.740 3.796 AT1G70860 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -296 -289 TCTCCCGT 5.2 6.7e-04 -7.308 3.174 AT1G75210 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -142 -135 CTTCCCGT 5.4 4.2e-04 -7.775 3.377 RPL32B site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -145 -138 TATCCCTC 5.2 5.9e-04 -7.435 3.229 TTG1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -486 -479 ATTACCGC 7.2 1.0e-04 -9.210 4.000 SCPL45 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -136 -129 TTTACCGC 7.6 4.7e-05 -9.965 4.328 SCPL45 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -10 -3 TTTCCCAC 6.9 2.1e-04 -8.468 3.678 BAD1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -397 -390 TATCCTGC 5.3 5.1e-04 -7.581 3.292 BAD1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -313 -306 TGTTCCGC 5.1 6.7e-04 -7.308 3.174 AT1G56740 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -286 -279 TTGCCCGC 8.1 2.3e-05 -10.680 4.638 NFYC2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -55 -48 CTTCCCGT 5.4 4.2e-04 -7.775 3.377 AT3G62790 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -134 -127 ATTCCTGC 6.7 2.5e-04 -8.294 3.602 AT3G62790 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -113 -106 TTACCCGT 5.3 5.1e-04 -7.581 3.292 LCR33 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -405 -398 ATACCCTC 4.7 9.5e-04 -6.959 3.022 LACS4 site 5015_E2Fb_Athamap_20091028_ D -499 -492 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 LACS4 site 5015_E2Fb_Athamap_20091028_ R -195 -188 TATCCCCC 4.9 7.5e-04 -7.195 3.125 DRP3A site 5015_E2Fb_Athamap_20091028_ D -499 -492 TGTCCCTC 4.8 7.5e-04 -7.195 3.125 AT1G08683 site 5015_E2Fb_Athamap_20091028_ D -145 -138 ATTCACGC 6.9 1.9e-04 -8.568 3.721 AT1G70860 site 5015_E2Fb_Athamap_20091028_ R -296 -289 TCTCCCGT 5.1 5.8e-04 -7.452 3.237 AT1G75210 site 5015_E2Fb_Athamap_20091028_ R -188 -181 TTTCGCGT 4.6 8.2e-04 -7.106 3.086 AT1G75210 site 5015_E2Fb_Athamap_20091028_ R -142 -135 CTTCCCGT 5.3 5.1e-04 -7.581 3.292 RPL32B site 5015_E2Fb_Athamap_20091028_ D -145 -138 TATCCCTC 5.1 5.8e-04 -7.452 3.237 TTG1 site 5015_E2Fb_Athamap_20091028_ D -486 -479 ATTACCGC 7.1 1.7e-04 -8.680 3.770 SCPL45 site 5015_E2Fb_Athamap_20091028_ D -136 -129 TTTACCGC 7.8 3.7e-05 -10.205 4.432 SCPL45 site 5015_E2Fb_Athamap_20091028_ R -10 -3 TTTCCCAC 7.1 1.7e-04 -8.680 3.770 BAD1 site 5015_E2Fb_Athamap_20091028_ R -397 -390 TATCCTGC 5.3 5.1e-04 -7.581 3.292 BAD1 site 5015_E2Fb_Athamap_20091028_ D -313 -306 TGTTCCGC 5.1 6.5e-04 -7.339 3.187 AT1G56740 site 5015_E2Fb_Athamap_20091028_ D -286 -279 TTGCCCGC 8.3 2.3e-05 -10.680 4.638 NFYC2 site 5015_E2Fb_Athamap_20091028_ D -55 -48 CTTCCCGT 5.3 5.1e-04 -7.581 3.292 AT3G62790 site 5015_E2Fb_Athamap_20091028_ D -134 -127 ATTCCTGC 6.6 2.5e-04 -8.294 3.602 AT3G62790 site 5015_E2Fb_Athamap_20091028_ R -113 -106 TTACCCGT 5.2 5.1e-04 -7.581 3.292 AT5G66510 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -466 -456 AACCCGTCAAA 6.2 2.3e-04 -8.377 3.638 AT5G48835 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -225 -215 TTCTCGTCCTT 5.2 5.0e-04 -7.601 3.301 AT5G48835 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -215 -205 ATCACGCTAGA 4.7 7.7e-04 -7.169 3.114 AT1G04083 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -47 -37 AACTCGCCAAG 4.5 9.1e-04 -7.002 3.041 LACS4 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -498 -488 TTCCCTCCACT 5.9 2.9e-04 -8.146 3.538 LACS4 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -38 -28 ATACGGCCCAA 4.7 7.7e-04 -7.169 3.114 SCPL50 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -385 -375 ATCCGGCGTAA 5.0 6.5e-04 -7.339 3.187 SCPL50 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -146 -136 TTTCGGCCCAA 5.3 4.6e-04 -7.684 3.337 AT1G08683 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -483 -473 AACCCTCTAAA 4.7 7.7e-04 -7.169 3.114 AT1G08683 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -415 -405 TTCCGTCGATA 4.5 9.1e-04 -7.002 3.041 AT1G08683 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -144 -134 TTCACGCGCTT 8.2 3.9e-05 -10.152 4.409 AT1G70860 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -403 -393 TACCGTCCCAA 4.6 9.1e-04 -7.002 3.041 AT1G75210 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -451 -441 TTCACGAGCTA 5.1 5.4e-04 -7.524 3.268 AT1G75210 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -191 -181 TTTACGCGAAA 4.9 6.5e-04 -7.339 3.187 AT2G02060 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -340 -330 TTCACTCCCAT 5.3 4.6e-04 -7.684 3.337 AT1G09487 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -464 -454 TATCTGCCCAA 4.5 9.1e-04 -7.002 3.041 RPL32B site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -106 -96 TTGCAGCCAAA 5.0 6.5e-04 -7.339 3.187 ECT7 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -109 -99 AACCCACGAAT 5.1 6.0e-04 -7.419 3.222 SCPL45 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -236 -226 TTATCGCCATA 5.8 3.1e-04 -8.079 3.509 BAD1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -401 -391 ATCCTGCCTTT 4.5 9.1e-04 -7.002 3.041 AT1G56740 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -286 -276 TGCGCGGGCAA 4.7 8.3e-04 -7.094 3.081 AT1G56740 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -285 -275 TGCCCGCGCAG 7.3 9.0e-05 -9.316 4.046 AT1G56740 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -268 -258 ATCCTGCCGTT 4.8 7.2e-04 -7.236 3.143 AT3G62790 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -133 -123 TTCCTGCTTAA 4.9 7.2e-04 -7.236 3.143 ; ; 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_ 19 0 ; 2 5015_E2Fb_Athamap_20091028_ 17 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 24 0 ; TOTAL 60 0 ; Host name rsat ; Job started 2026-08-17.163145 ; Job done 2026-08-17.163146 ; Seconds 0.45 ; user 0.45 ; system 0.03 ; cuser 0.73 ; csystem 0.13