; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.172633_7gXGLG.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_2026-08-17.172633_gDjXmO.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.172633_gDjXmO.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_2026-08-17.172633_7gXGLG.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 ATCG00620|TRNP limit START_END D -500 -1 . 0 0 0 0 AT1G75070|AT1G75070 limit START_END D -500 -1 . 0 0 0 0 AT5G25580|AT5G25580 limit START_END D -500 -1 . 0 0 0 0 AT3G45610|DOF3.2 limit START_END D -500 -1 . 0 0 0 0 AT2G12480|SCPL43 limit START_END D -500 -1 . 0 0 0 0 AT1G01580|FRO2 limit START_END D -500 -1 . 0 0 0 0 AT1G18480|SLP2 limit START_END D -500 -1 . 0 0 0 0 AT1G18773|AT1G18773 limit START_END D -500 -1 . 0 0 0 0 AT5G62810|PEX14 limit START_END D -500 -1 . 0 0 0 0 ATMG00160|COX2 limit START_END D -500 -1 . 0 0 0 0 AT4G33680|DAP limit START_END D -500 -1 . 0 0 0 0 AT1G33170|AT1G33170 limit START_END D -500 -1 . 0 0 0 0 AT1G66810|AT1G66810 limit START_END D -500 -1 . 0 0 0 0 AT4G06526|AT4G06526 limit START_END D -500 -1 . 0 0 0 0 AT3G04490|AT3G04490 limit START_END D -500 -1 . 0 0 0 0 AT3G05936|AT3G05936 limit START_END D -500 -1 . 0 0 0 0 AT1G52500|FPG1 limit START_END D -500 -1 . 0 0 0 0 AT5G42970|CSN4 limit START_END D -500 -1 . 0 0 0 0 AT1G60560|AT1G60560 limit START_END D -500 -1 . 0 0 0 0 AT2G39430|DIR9 limit START_END D -500 -1 . 0 0 0 0 AT1G71310|RAD52-1 limit START_END D -500 -1 . 0 0 0 0 AT5G26617|AT5G26617 limit START_END D -500 -1 . 0 0 0 0 AT2G34260|WDR55 limit START_END D -500 -1 . 0 0 0 0 AT1G44446|CAO limit START_END D -500 -1 . 0 0 0 0 AT1G75070|AT1G75070 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -395 -388 AATCACGC 4.8 9.5e-04 -6.959 3.022 AT1G75070|AT1G75070 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -76 -69 ATACCAGC 4.9 8.8e-04 -7.036 3.056 AT3G45610|DOF3.2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -34 -27 ATTCCCTC 6.6 2.6e-04 -8.255 3.585 AT5G62810|PEX14 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -356 -349 GTTCCCGG 5.3 5.9e-04 -7.435 3.229 AT4G33680|DAP site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -144 -137 TTTCCAGC 7.1 1.4e-04 -8.874 3.854 AT1G33170|AT1G33170 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -254 -247 TGTCCCAC 4.8 8.8e-04 -7.036 3.056 AT4G06526|AT4G06526 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -444 -437 ACTCCCGC 7.7 3.5e-05 -10.260 4.456 AT4G06526|AT4G06526 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -163 -156 CTTCCCAC 5.1 6.7e-04 -7.308 3.174 AT4G06526|AT4G06526 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -139 -132 TTTCCGGC 7.2 1.0e-04 -9.210 4.000 AT4G06526|AT4G06526 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -75 -68 TTTCCGGC 7.2 1.0e-04 -9.210 4.000 AT4G06526|AT4G06526 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -27 -20 TATCCCCC 4.9 8.0e-04 -7.131 3.097 AT3G05936|AT3G05936 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -290 -283 TTTTCCGC 7.2 1.0e-04 -9.210 4.000 AT1G52500|FPG1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -491 -484 CTTCACGC 5.6 3.5e-04 -7.958 3.456 AT1G60560|AT1G60560 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -114 -107 TTCCCCGA 4.8 8.8e-04 -7.036 3.056 AT1G71310|RAD52-1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -100 -93 CGTCCCGC 6.5 2.7e-04 -8.217 3.569 AT2G34260|WDR55 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -135 -128 TCTCCGGC 5.2 5.9e-04 -7.435 3.229 AT2G34260|WDR55 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -128 -121 CGTCCCGC 6.5 2.7e-04 -8.217 3.569 AT1G44446|CAO site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -60 -53 AATACCGC 5.0 8.0e-04 -7.131 3.097 AT1G44446|CAO site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -22 -15 CTTCCCGA 5.3 5.1e-04 -7.581 3.292 AT3G45610|DOF3.2 site 5015_E2Fb_Athamap_20091028_ D -34 -27 ATTCCCTC 6.4 2.6e-04 -8.255 3.585 AT5G62810|PEX14 site 5015_E2Fb_Athamap_20091028_ D -356 -349 GTTCCCGG 5.1 5.8e-04 -7.452 3.237 AT4G33680|DAP site 5015_E2Fb_Athamap_20091028_ D -144 -137 TTTCCAGC 7.3 1.3e-04 -8.948 3.886 AT1G33170|AT1G33170 site 5015_E2Fb_Athamap_20091028_ D -413 -406 TTCCCCTC 4.6 8.2e-04 -7.106 3.086 AT1G33170|AT1G33170 site 5015_E2Fb_Athamap_20091028_ R -254 -247 TGTCCCAC 4.7 7.9e-04 -7.143 3.102 AT4G06526|AT4G06526 site 5015_E2Fb_Athamap_20091028_ R -444 -437 ACTCCCGC 7.6 5.8e-05 -9.755 4.237 AT4G06526|AT4G06526 site 5015_E2Fb_Athamap_20091028_ R -163 -156 CTTCCCAC 5.0 6.9e-04 -7.279 3.161 AT4G06526|AT4G06526 site 5015_E2Fb_Athamap_20091028_ R -139 -132 TTTCCGGC 7.4 9.3e-05 -9.283 4.032 AT4G06526|AT4G06526 site 5015_E2Fb_Athamap_20091028_ R -75 -68 TTTCCGGC 7.4 9.3e-05 -9.283 4.032 AT4G06526|AT4G06526 site 5015_E2Fb_Athamap_20091028_ R -27 -20 TATCCCCC 4.9 7.5e-04 -7.195 3.125 AT3G05936|AT3G05936 site 5015_E2Fb_Athamap_20091028_ D -290 -283 TTTTCCGC 7.4 9.3e-05 -9.283 4.032 AT1G52500|FPG1 site 5015_E2Fb_Athamap_20091028_ R -491 -484 CTTCACGC 5.5 3.6e-04 -7.929 3.444 AT1G60560|AT1G60560 site 5015_E2Fb_Athamap_20091028_ D -114 -107 TTCCCCGA 4.8 7.9e-04 -7.143 3.102 AT1G71310|RAD52-1 site 5015_E2Fb_Athamap_20091028_ R -100 -93 CGTCCCGC 6.4 2.7e-04 -8.217 3.569 AT2G34260|WDR55 site 5015_E2Fb_Athamap_20091028_ D -135 -128 TCTCCGGC 5.1 5.8e-04 -7.452 3.237 AT2G34260|WDR55 site 5015_E2Fb_Athamap_20091028_ D -128 -121 CGTCCCGC 6.4 2.7e-04 -8.217 3.569 AT1G44446|CAO site 5015_E2Fb_Athamap_20091028_ D -60 -53 AATACCGC 4.5 9.4e-04 -6.970 3.027 AT1G44446|CAO site 5015_E2Fb_Athamap_20091028_ D -22 -15 CTTCCCGA 5.2 5.1e-04 -7.581 3.292 ATCG00620|TRNP site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -254 -244 TCCCCCCGCTT 4.7 7.7e-04 -7.169 3.114 AT1G75070|AT1G75070 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -21 -11 ATCGAGCGATT 5.3 4.6e-04 -7.684 3.337 AT1G75070|AT1G75070 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -20 -10 ATCGCTCGATT 5.3 4.6e-04 -7.684 3.337 AT5G25580|AT5G25580 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -159 -149 TTACGGCCCAA 5.7 3.3e-04 -8.016 3.481 AT2G12480|SCPL43 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -328 -318 AACACGCTCAA 5.5 3.9e-04 -7.849 3.409 AT1G01580|FRO2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -440 -430 TACACGCTATG 4.5 9.1e-04 -7.002 3.041 AT5G62810|PEX14 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -286 -276 TTCCTGAGCAA 4.4 9.8e-04 -6.928 3.009 AT5G62810|PEX14 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -134 -124 TTAGCGTCCAT 4.5 9.1e-04 -7.002 3.041 ATMG00160|COX2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -139 -129 TACGCCCCAAA 6.4 1.9e-04 -8.568 3.721 ATMG00160|COX2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -40 -30 CTCCCCCCAAA 5.5 3.9e-04 -7.849 3.409 AT4G33680|DAP site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -232 -222 ATCTCGACCAA 4.8 7.2e-04 -7.236 3.143 AT4G33680|DAP site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -165 -155 ATCGCACGATT 5.3 5.0e-04 -7.601 3.301 AT4G33680|DAP site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -164 -154 ATCGTGCGATT 5.3 5.0e-04 -7.601 3.301 AT1G66810|AT1G66810 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -240 -230 TTCCATCCCAA 5.1 5.4e-04 -7.524 3.268 AT4G06526|AT4G06526 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -167 -157 TTCCCACTATG 4.5 9.1e-04 -7.002 3.041 AT4G06526|AT4G06526 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -142 -132 TTTCCGGCATT 4.4 9.8e-04 -6.928 3.009 AT3G05936|AT3G05936 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -478 -468 TTCCCAACAAA 4.6 8.3e-04 -7.094 3.081 AT3G05936|AT3G05936 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -289 -279 TTTCCGCAAAA 5.4 4.2e-04 -7.775 3.377 AT5G26617|AT5G26617 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -497 -487 TTCGCACCAAA 7.3 9.0e-05 -9.316 4.046 AT2G34260|WDR55 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -127 -117 GTCCCGCTAAT 8.2 3.4e-05 -10.289 4.469 ; ; 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_ 19 0 ; 2 5015_E2Fb_Athamap_20091028_ 18 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 20 0 ; TOTAL 57 0 ; Host name rsat ; Job started 2026-08-17.172633 ; Job done 2026-08-17.172635 ; Seconds 0.44 ; user 0.44 ; system 0.04 ; cuser 0.78 ; csystem 0.1