; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.164053_siOfCs.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_2026-08-17.164053_onjQTg.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_2026-08-17.164053_onjQTg.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.164053_siOfCs.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 ARID6 limit START_END D -500 -1 . 0 0 0 0 EDL3 limit START_END D -500 -1 . 0 0 0 0 U2.3 limit START_END D -500 -1 . 0 0 0 0 CGL160 limit START_END D -500 -1 . 0 0 0 0 NAC031 limit START_END D -500 -1 . 0 0 0 0 AT5G06595 limit START_END D -500 -1 . 0 0 0 0 AT5G37474 limit START_END D -500 -1 . 0 0 0 0 AT1G71070 limit START_END D -500 -1 . 0 0 0 0 BRXL1 limit START_END D -500 -1 . 0 0 0 0 AT2G27540 limit START_END D -500 -1 . 0 0 0 0 AT1G64830 limit START_END D -500 -1 . 0 0 0 0 SKIP34 limit START_END D -500 -1 . 0 0 0 0 PXC3 limit START_END D -500 -1 . 0 0 0 0 AT5G45480 limit START_END D -500 -1 . 0 0 0 0 AT3G57850 limit START_END D -500 -1 . 0 0 0 0 PCMP-E72 limit START_END D -500 -1 . 0 0 0 0 AT2G45320 limit START_END D -500 -1 . 0 0 0 0 AT3G05595 limit START_END D -500 -1 . 0 0 0 0 AT1G71900 limit START_END D -500 -1 . 0 0 0 0 AT1G58007 limit START_END D -500 -1 . 0 0 0 0 AT3G04980 limit START_END D -500 -1 . 0 0 0 0 AT4G38560 limit START_END D -500 -1 . 0 0 0 0 SWEET13 limit START_END D -500 -1 . 0 0 0 0 AT4G24275 limit START_END D -500 -1 . 0 0 0 0 MAP70.1 limit START_END D -500 -1 . 0 0 0 0 COG0212 limit START_END D -500 -1 . 0 0 0 0 CYP77A5P limit START_END D -500 -1 . 0 0 0 0 AT2G20440 limit START_END D -500 -1 . 0 0 0 0 EDL3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -490 -483 TCTCCCTC 4.9 8.0e-04 -7.131 3.097 EDL3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -369 -362 TTACACGC 5.5 3.9e-04 -7.849 3.409 EDL3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -93 -86 GTTCCCGA 5.3 5.1e-04 -7.581 3.292 U2.3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -141 -134 TGTCCCGC 8.1 2.3e-05 -10.680 4.638 U2.3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -110 -103 TCTCCCTC 4.9 8.0e-04 -7.131 3.097 CGL160 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -216 -209 TGTCCCAC 4.8 8.8e-04 -7.036 3.056 NAC031 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -179 -172 TTTCCCGT 7.2 1.4e-04 -8.874 3.854 NAC031 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -90 -83 TTGCCCTC 4.8 8.8e-04 -7.036 3.056 AT5G37474 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -477 -470 TTTCTCGC 7.4 6.6e-05 -9.626 4.180 AT5G37474 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -399 -392 TTATCCGC 5.4 4.2e-04 -7.775 3.377 AT1G71070 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -134 -127 CTTCACGC 5.6 3.5e-04 -7.958 3.456 AT1G71070 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -88 -81 ATACACGC 5.2 6.7e-04 -7.308 3.174 BRXL1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -234 -227 CTTCCTGC 5.3 5.1e-04 -7.581 3.292 AT2G27540 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -211 -204 TCTCCAGC 5.1 6.7e-04 -7.308 3.174 AT2G27540 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -205 -198 ATCTCCGC 4.8 8.8e-04 -7.036 3.056 AT2G27540 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -12 -5 TGTCCCAC 4.8 8.8e-04 -7.036 3.056 SKIP34 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -431 -424 ATCTCCGC 4.8 8.8e-04 -7.036 3.056 SKIP34 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -366 -359 CTTCCCGT 5.4 4.2e-04 -7.775 3.377 PXC3 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -55 -48 ATTCCCTC 6.6 2.6e-04 -8.255 3.585 AT5G45480 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -475 -468 TTTCCCGT 7.2 1.4e-04 -8.874 3.854 PCMP-E72 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -401 -394 TTAGCCGC 5.5 3.9e-04 -7.849 3.409 AT2G45320 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -485 -478 CTTTCCGC 5.4 4.2e-04 -7.775 3.377 AT2G45320 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -363 -356 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 AT1G71900 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -223 -216 TTTCTCGC 7.4 6.6e-05 -9.626 4.180 AT1G58007 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -160 -153 ATTTCCGC 6.8 2.1e-04 -8.468 3.678 AT3G04980 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -34 -27 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 AT3G04980 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -11 -4 CTTCCCTC 5.2 5.9e-04 -7.435 3.229 MAP70.1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -290 -283 TGTCCCTC 4.9 8.8e-04 -7.036 3.056 MAP70.1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -178 -171 GTTCCCTC 5.2 6.7e-04 -7.308 3.174 MAP70.1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -169 -162 TCTCACGC 5.4 4.2e-04 -7.775 3.377 COG0212 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -236 -229 AAACCCGC 5.2 6.7e-04 -7.308 3.174 COG0212 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -165 -158 TTACCCGT 5.3 5.1e-04 -7.581 3.292 CYP77A5P site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -195 -188 CTTACCGC 5.9 3.1e-04 -8.079 3.509 AT2G20440 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -439 -432 ATCCTCGC 4.8 8.8e-04 -7.036 3.056 AT2G20440 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -190 -183 TTCGCCGC 5.4 4.2e-04 -7.775 3.377 EDL3 site 5015_E2Fb_Athamap_20091028_ R -490 -483 TCTCCCTC 4.8 7.5e-04 -7.195 3.125 EDL3 site 5015_E2Fb_Athamap_20091028_ D -369 -362 TTACACGC 5.5 3.9e-04 -7.849 3.409 EDL3 site 5015_E2Fb_Athamap_20091028_ D -93 -86 GTTCCCGA 5.2 5.1e-04 -7.581 3.292 U2.3 site 5015_E2Fb_Athamap_20091028_ D -141 -134 TGTCCCGC 8.3 2.3e-05 -10.680 4.638 U2.3 site 5015_E2Fb_Athamap_20091028_ D -110 -103 TCTCCCTC 4.8 7.5e-04 -7.195 3.125 CGL160 site 5015_E2Fb_Athamap_20091028_ R -216 -209 TGTCCCAC 4.7 7.9e-04 -7.143 3.102 NAC031 site 5015_E2Fb_Athamap_20091028_ R -179 -172 TTTCCCGT 7.4 1.3e-04 -8.948 3.886 NAC031 site 5015_E2Fb_Athamap_20091028_ R -90 -83 TTGCCCTC 4.7 7.9e-04 -7.143 3.102 AT5G37474 site 5015_E2Fb_Athamap_20091028_ D -477 -470 TTTCTCGC 7.6 5.8e-05 -9.755 4.237 AT5G37474 site 5015_E2Fb_Athamap_20091028_ D -399 -392 TTATCCGC 5.4 3.9e-04 -7.849 3.409 AT1G71070 site 5015_E2Fb_Athamap_20091028_ R -134 -127 CTTCACGC 5.5 3.6e-04 -7.929 3.444 AT1G71070 site 5015_E2Fb_Athamap_20091028_ R -88 -81 ATACACGC 4.7 7.9e-04 -7.143 3.102 BRXL1 site 5015_E2Fb_Athamap_20091028_ D -234 -227 CTTCCTGC 5.2 5.1e-04 -7.581 3.292 AT2G27540 site 5015_E2Fb_Athamap_20091028_ D -211 -204 TCTCCAGC 5.0 6.5e-04 -7.339 3.187 AT2G27540 site 5015_E2Fb_Athamap_20091028_ R -12 -5 TGTCCCAC 4.7 7.9e-04 -7.143 3.102 SKIP34 site 5015_E2Fb_Athamap_20091028_ D -366 -359 CTTCCCGT 5.3 5.1e-04 -7.581 3.292 PXC3 site 5015_E2Fb_Athamap_20091028_ D -55 -48 ATTCCCTC 6.4 2.6e-04 -8.255 3.585 AT5G45480 site 5015_E2Fb_Athamap_20091028_ D -475 -468 TTTCCCGT 7.4 1.3e-04 -8.948 3.886 PCMP-E72 site 5015_E2Fb_Athamap_20091028_ R -401 -394 TTAGCCGC 5.5 3.9e-04 -7.849 3.409 AT2G45320 site 5015_E2Fb_Athamap_20091028_ D -485 -478 CTTTCCGC 5.3 4.4e-04 -7.729 3.357 AT2G45320 site 5015_E2Fb_Athamap_20091028_ R -363 -356 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 AT1G71900 site 5015_E2Fb_Athamap_20091028_ R -223 -216 TTTCTCGC 7.6 5.8e-05 -9.755 4.237 AT1G58007 site 5015_E2Fb_Athamap_20091028_ D -160 -153 ATTTCCGC 6.7 2.1e-04 -8.468 3.678 AT3G04980 site 5015_E2Fb_Athamap_20091028_ D -34 -27 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 AT3G04980 site 5015_E2Fb_Athamap_20091028_ D -11 -4 CTTCCCTC 5.0 6.5e-04 -7.339 3.187 MAP70.1 site 5015_E2Fb_Athamap_20091028_ D -290 -283 TGTCCCTC 4.8 7.5e-04 -7.195 3.125 MAP70.1 site 5015_E2Fb_Athamap_20091028_ D -178 -171 GTTCCCTC 5.0 6.5e-04 -7.339 3.187 MAP70.1 site 5015_E2Fb_Athamap_20091028_ D -169 -162 TCTCACGC 5.3 4.4e-04 -7.729 3.357 COG0212 site 5015_E2Fb_Athamap_20091028_ D -236 -229 AAACCCGC 4.8 7.9e-04 -7.143 3.102 COG0212 site 5015_E2Fb_Athamap_20091028_ D -165 -158 TTACCCGT 5.2 5.1e-04 -7.581 3.292 CYP77A5P site 5015_E2Fb_Athamap_20091028_ R -195 -188 CTTACCGC 5.7 3.1e-04 -8.079 3.509 AT2G20440 site 5015_E2Fb_Athamap_20091028_ R -190 -183 TTCGCCGC 5.4 4.4e-04 -7.729 3.357 EDL3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -92 -82 TTCCCGATCTT 6.8 1.5e-04 -8.805 3.824 U2.3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -330 -320 TCCTCGCCCCA 4.5 9.8e-04 -6.928 3.009 U2.3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -328 -318 CTCGCCCCAAA 4.8 7.2e-04 -7.236 3.143 U2.3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -270 -260 AACCGGCTAAT 4.8 7.2e-04 -7.236 3.143 U2.3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -241 -231 TTCCTGTCAAA 4.9 7.2e-04 -7.236 3.143 U2.3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -140 -130 GTCCCGCAAAC 4.4 9.8e-04 -6.928 3.009 U2.3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -56 -46 TTCTCGTCCAA 5.8 3.1e-04 -8.079 3.509 AT5G06595 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -172 -162 ATCGCGTCTTA 4.6 8.3e-04 -7.094 3.081 AT5G37474 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -476 -466 TTCTCGCCAAG 6.8 1.4e-04 -8.874 3.854 AT5G37474 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -398 -388 TATCCGCCAAA 7.8 5.3e-05 -9.845 4.276 AT1G71070 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -138 -128 TTCACGCGCTT 8.2 3.9e-05 -10.152 4.409 AT1G71070 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -92 -82 TACACGCTCTT 6.5 1.8e-04 -8.623 3.745 BRXL1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -491 -481 TTCCCTACATA 5.2 5.0e-04 -7.601 3.301 PXC3 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -54 -44 TTCCCTCCTTT 5.3 4.6e-04 -7.684 3.337 AT5G45480 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -213 -203 TTCCCTTCATA 4.8 7.2e-04 -7.236 3.143 PCMP-E72 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -318 -308 TACCCTACATA 4.5 9.8e-04 -6.928 3.009 AT2G45320 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -367 -357 TTCCCTCGTTT 4.6 8.3e-04 -7.094 3.081 AT1G58007 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -405 -395 ATCGAGCTAAT 5.1 5.4e-04 -7.524 3.268 AT3G04980 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -33 -23 TTCCCTCCTTA 6.0 2.7e-04 -8.217 3.569 SWEET13 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -33 -23 AACCCTCTATA 4.9 6.5e-04 -7.339 3.187 MAP70.1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -168 -158 CTCACGCGCAA 6.4 2.1e-04 -8.468 3.678 COG0212 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -235 -225 AACCCGCTCTT 8.1 4.3e-05 -10.054 4.367 COG0212 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -222 -212 TACTCGCGTTT 4.6 8.3e-04 -7.094 3.081 COG0212 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -193 -183 CACGCGCTCTT 6.0 2.7e-04 -8.217 3.569 COG0212 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -164 -154 TACCCGTCCAA 8.1 3.9e-05 -10.152 4.409 COG0212 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -140 -130 TACACGCGCTA 8.1 4.3e-05 -10.054 4.367 COG0212 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -57 -47 TATCTGCCCAA 4.5 9.1e-04 -7.002 3.041 CYP77A5P site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -247 -237 ATCCCGTAAAT 4.5 9.1e-04 -7.002 3.041 AT2G20440 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -438 -428 TCCTCGCCGTA 4.5 9.1e-04 -7.002 3.041 AT2G20440 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -226 -216 AGCCGGCCAAA 5.0 6.0e-04 -7.419 3.222 AT2G20440 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -225 -215 TAGCCGGCCAA 4.7 7.7e-04 -7.169 3.114 ; ; 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_ 35 0 ; 2 5015_E2Fb_Athamap_20091028_ 32 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 31 0 ; TOTAL 98 0 ; Host name rsat ; Job started 2026-08-17.164054 ; Job done 2026-08-17.164055 ; Seconds 0.48 ; user 0.48 ; system 0.04 ; cuser 0.76 ; csystem 0.08