; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.115618_JYZvM3.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_2026-08-17.115618_x361s7.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_2026-08-17.115618_x361s7.fasta ; Matrix files ; matrix 1 $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.115618_JYZvM3.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 AT1G05757 limit START_END D -500 -1 . 0 0 0 0 AT5G07395 limit START_END D -500 -1 . 0 0 0 0 LIP2 limit START_END D -500 -1 . 0 0 0 0 AT1G70180 limit START_END D -500 -1 . 0 0 0 0 AT1G16025 limit START_END D -500 -1 . 0 0 0 0 COP1 limit START_END D -500 -1 . 0 0 0 0 DEP limit START_END D -500 -1 . 0 0 0 0 SINE1 limit START_END D -500 -1 . 0 0 0 0 VPS2.1 limit START_END D -500 -1 . 0 0 0 0 AT3G52105 limit START_END D -500 -1 . 0 0 0 0 AT3G60415 limit START_END D -500 -1 . 0 0 0 0 AT4G27530 limit START_END D -500 -1 . 0 0 0 0 AT3G23860 limit START_END D -500 -1 . 0 0 0 0 DTX7 limit START_END D -500 -1 . 0 0 0 0 AT3G12835 limit START_END D -500 -1 . 0 0 0 0 CP12-1 limit START_END D -500 -1 . 0 0 0 0 AT4G16140 limit START_END D -500 -1 . 0 0 0 0 KRP3 limit START_END D -500 -1 . 0 0 0 0 AT4G40063 limit START_END D -500 -1 . 0 0 0 0 AT4G05545 limit START_END D -500 -1 . 0 0 0 0 AT2G23755 limit START_END D -500 -1 . 0 0 0 0 AT5G57250 limit START_END D -500 -1 . 0 0 0 0 KMS1 limit START_END D -500 -1 . 0 0 0 0 AT5G03165 limit START_END D -500 -1 . 0 0 0 0 AT1G05757 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -283 -276 ATACCCTC 4.7 9.5e-04 -6.959 3.022 AT1G70180 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -358 -351 TTTCCGGC 7.2 1.0e-04 -9.210 4.000 AT1G16025 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -30 -23 TTCTCCGC 5.2 5.9e-04 -7.435 3.229 COP1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -404 -397 GTTCCCTC 5.2 6.7e-04 -7.308 3.174 COP1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -117 -110 TATCCGGC 5.5 4.2e-04 -7.775 3.377 COP1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -70 -63 TTTCGCGC 7.7 3.5e-05 -10.260 4.456 DEP site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -184 -177 ATATCCGC 5.1 6.7e-04 -7.308 3.174 AT3G52105 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -440 -433 CTTCCCGA 5.3 5.1e-04 -7.581 3.292 AT3G52105 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -118 -111 TTATCCGC 5.4 4.2e-04 -7.775 3.377 AT3G60415 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -129 -122 TTCCTCGC 5.2 5.9e-04 -7.435 3.229 AT4G27530 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -308 -301 TGTACCGC 5.5 3.9e-04 -7.849 3.409 AT4G27530 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -85 -78 TCTCCCGA 5.1 6.7e-04 -7.308 3.174 AT3G12835 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -353 -346 TTGCCCTC 4.8 8.8e-04 -7.036 3.056 AT3G12835 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -42 -35 TCTCCCTC 4.9 8.0e-04 -7.131 3.097 CP12-1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -41 -34 TTCCCCGG 4.7 9.5e-04 -6.959 3.022 AT4G05545 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -499 -492 TCTGCCGC 5.3 5.1e-04 -7.581 3.292 AT4G05545 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -416 -409 CTTCCCGG 5.3 5.9e-04 -7.435 3.229 AT4G05545 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -386 -379 CTTACCGC 5.9 3.1e-04 -8.079 3.509 AT4G05545 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -57 -50 TCTCCCAC 4.9 8.8e-04 -7.036 3.056 AT2G23755 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -215 -208 ATACCTGC 4.9 8.8e-04 -7.036 3.056 AT5G57250 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -267 -260 TGTCCAGC 5.0 7.4e-04 -7.209 3.131 AT5G03165 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -446 -439 GTTCCCGG 5.3 5.9e-04 -7.435 3.229 AT5G03165 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -416 -409 TTCACCGC 5.1 6.7e-04 -7.308 3.174 AT5G03165 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -257 -250 AGTACCGC 5.1 6.7e-04 -7.308 3.174 AT1G70180 site 5015_E2Fb_Athamap_20091028_ D -358 -351 TTTCCGGC 7.4 9.3e-05 -9.283 4.032 AT1G16025 site 5015_E2Fb_Athamap_20091028_ R -30 -23 TTCTCCGC 5.1 5.8e-04 -7.452 3.237 COP1 site 5015_E2Fb_Athamap_20091028_ R -404 -397 GTTCCCTC 5.0 6.5e-04 -7.339 3.187 COP1 site 5015_E2Fb_Athamap_20091028_ R -117 -110 TATCCGGC 5.4 3.9e-04 -7.849 3.409 COP1 site 5015_E2Fb_Athamap_20091028_ R -70 -63 TTTCGCGC 7.9 2.8e-05 -10.483 4.553 DEP site 5015_E2Fb_Athamap_20091028_ D -184 -177 ATATCCGC 4.7 8.2e-04 -7.106 3.086 AT3G52105 site 5015_E2Fb_Athamap_20091028_ R -440 -433 CTTCCCGA 5.2 5.1e-04 -7.581 3.292 AT3G52105 site 5015_E2Fb_Athamap_20091028_ R -118 -111 TTATCCGC 5.4 3.9e-04 -7.849 3.409 AT3G60415 site 5015_E2Fb_Athamap_20091028_ D -129 -122 TTCCTCGC 5.1 5.8e-04 -7.452 3.237 AT4G27530 site 5015_E2Fb_Athamap_20091028_ R -308 -301 TGTACCGC 5.5 3.9e-04 -7.849 3.409 AT4G27530 site 5015_E2Fb_Athamap_20091028_ D -85 -78 TCTCCCGA 5.0 6.5e-04 -7.339 3.187 AT3G23860 site 5015_E2Fb_Athamap_20091028_ D -160 -153 TCTCCCCC 4.6 8.2e-04 -7.106 3.086 AT3G12835 site 5015_E2Fb_Athamap_20091028_ D -353 -346 TTGCCCTC 4.7 7.9e-04 -7.143 3.102 AT3G12835 site 5015_E2Fb_Athamap_20091028_ R -42 -35 TCTCCCTC 4.8 7.5e-04 -7.195 3.125 CP12-1 site 5015_E2Fb_Athamap_20091028_ R -41 -34 TTCCCCGG 4.7 8.2e-04 -7.106 3.086 AT4G05545 site 5015_E2Fb_Athamap_20091028_ D -499 -492 TCTGCCGC 5.3 5.1e-04 -7.581 3.292 AT4G05545 site 5015_E2Fb_Athamap_20091028_ D -416 -409 CTTCCCGG 5.1 5.8e-04 -7.452 3.237 AT4G05545 site 5015_E2Fb_Athamap_20091028_ D -386 -379 CTTACCGC 5.7 3.1e-04 -8.079 3.509 AT4G05545 site 5015_E2Fb_Athamap_20091028_ R -57 -50 TCTCCCAC 4.8 7.5e-04 -7.195 3.125 AT5G57250 site 5015_E2Fb_Athamap_20091028_ D -267 -260 TGTCCAGC 4.9 6.9e-04 -7.279 3.161 AT5G03165 site 5015_E2Fb_Athamap_20091028_ D -446 -439 GTTCCCGG 5.1 5.8e-04 -7.452 3.237 AT5G03165 site 5015_E2Fb_Athamap_20091028_ D -416 -409 TTCACCGC 5.1 6.5e-04 -7.339 3.187 AT5G03165 site 5015_E2Fb_Athamap_20091028_ R -257 -250 AGTACCGC 4.7 7.9e-04 -7.143 3.102 LIP2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -54 -44 ATCCCTCCACT 4.9 6.5e-04 -7.339 3.187 AT1G70180 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -358 -348 TTTCCGGCAAT 4.8 7.2e-04 -7.236 3.143 AT1G70180 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -357 -347 TTCCGGCAATA 5.6 3.6e-04 -7.929 3.444 COP1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -408 -398 TTCCCTCCATT 7.7 6.6e-05 -9.626 4.180 COP1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -100 -90 TACCAGCGCTT 6.9 1.3e-04 -8.948 3.886 COP1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -74 -64 TTCGCGCGTGT 5.9 2.9e-04 -8.146 3.538 COP1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -73 -63 CACGCGCGAAA 6.9 1.3e-04 -8.948 3.886 SINE1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -108 -98 TCACCGCTCTA 5.2 5.0e-04 -7.601 3.301 AT3G52105 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -444 -434 TTCCCGAGCTC 5.7 3.6e-04 -7.929 3.444 AT4G27530 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -312 -302 GTACCGCTCTT 4.9 7.2e-04 -7.236 3.143 AT4G27530 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -229 -219 TTCGGGCCCTT 7.0 1.3e-04 -8.948 3.886 AT3G23860 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -423 -413 AACCCTCTCAT 4.7 7.7e-04 -7.169 3.114 AT3G23860 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -341 -331 AACACGCCAAA 6.6 1.8e-04 -8.623 3.745 AT3G23860 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -161 -151 TTCTCCCCCAA 5.2 5.0e-04 -7.601 3.301 AT4G16140 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -379 -369 TTCCCAACAAA 4.6 8.3e-04 -7.094 3.081 AT4G05545 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -385 -375 TTACCGCTTTA 5.0 6.0e-04 -7.419 3.222 AT2G23755 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -475 -465 ATACGGCCCTA 4.8 7.2e-04 -7.236 3.143 AT2G23755 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -135 -125 TGAGCGCCATT 4.5 9.1e-04 -7.002 3.041 AT5G57250 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -383 -373 ATCCCGAGATA 6.8 1.5e-04 -8.805 3.824 KMS1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -79 -69 AACGTGCCATT 4.6 8.3e-04 -7.094 3.081 AT5G03165 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -425 -415 AACTCGCCAAG 4.5 9.1e-04 -7.002 3.041 ; ; 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_ 24 0 ; 2 5015_E2Fb_Athamap_20091028_ 23 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 21 0 ; TOTAL 68 0 ; Host name rsat ; Job started 2026-08-17.115618 ; Job done 2026-08-17.115619 ; Seconds 0.49 ; user 0.49 ; system 0.04 ; cuser 0.75 ; csystem 0.1