; matrix-scan -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/08/17/matrix-scan_2026-08-17.164440_ipVrOv.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_2026-08-17.164440_TgiEVp.fasta -seq_format fasta -n score ; Quick counting mode ; Input files ; input $RSAT/public_html/tmp/www-data/2026/08/17/tmp_sequence_2026-08-17.164440_TgiEVp.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_2026-08-17.164440_ipVrOv.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 PUB24 limit START_END D -500 -1 . 0 0 0 0 MLP423 limit START_END D -500 -1 . 0 0 0 0 MYB1 limit START_END D -500 -1 . 0 0 0 0 CALS5 limit START_END D -500 -1 . 0 0 0 0 RCCR limit START_END D -500 -1 . 0 0 0 0 AT1G21770 limit START_END D -500 -1 . 0 0 0 0 AT1G24220 limit START_END D -500 -1 . 0 0 0 0 AT4G22390 limit START_END D -500 -1 . 0 0 0 0 AT5G50180 limit START_END D -500 -1 . 0 0 0 0 AT5G39530 limit START_END D -500 -1 . 0 0 0 0 AT3G43150 limit START_END D -500 -1 . 0 0 0 0 AT2G14510 limit START_END D -500 -1 . 0 0 0 0 AT1G68875 limit START_END D -500 -1 . 0 0 0 0 ARAC9 limit START_END D -500 -1 . 0 0 0 0 PAS2 limit START_END D -500 -1 . 0 0 0 0 AT1G08057 limit START_END D -500 -1 . 0 0 0 0 AT2G27790 limit START_END D -500 -1 . 0 0 0 0 AT1G04177 limit START_END D -500 -1 . 0 0 0 0 AT2G30560 limit START_END D -500 -1 . 0 0 0 0 LHCB2.2 limit START_END D -500 -1 . 0 0 0 0 AAE6 limit START_END D -500 -1 . 0 0 0 0 AT3G47940 limit START_END D -500 -1 . 0 0 0 0 AT5G24670 limit START_END D -500 -1 . 0 0 0 0 ABH1 limit START_END D -500 -1 . 0 0 0 0 MTM2 limit START_END D -500 -1 . 0 0 0 0 AT5G05695 limit START_END D -500 -1 . 0 0 0 0 MSR4 limit START_END D -500 -1 . 0 0 0 0 MENG limit START_END D -500 -1 . 0 0 0 0 MYB1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -182 -175 TTTCCCGC 10.2 4.7e-06 -12.268 5.328 MYB1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -118 -111 TATCCCCC 4.9 8.0e-04 -7.131 3.097 CALS5 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -490 -483 TGTCACGC 5.3 5.1e-04 -7.581 3.292 CALS5 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -27 -20 TTTCCCTC 6.9 1.9e-04 -8.568 3.721 AT1G21770 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -139 -132 CTTCACGC 5.6 3.5e-04 -7.958 3.456 AT1G21770 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -102 -95 TCTGCCGC 5.3 5.1e-04 -7.581 3.292 AT4G22390 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -395 -388 CTTCCCTC 5.2 5.9e-04 -7.435 3.229 AT4G22390 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -214 -207 TCTCCCGC 8.2 1.9e-05 -10.871 4.721 AT5G50180 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -378 -371 TGTCCCAC 4.8 8.8e-04 -7.036 3.056 AT5G39530 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -369 -362 CTTCCCAC 5.1 6.7e-04 -7.308 3.174 AT3G43150 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -152 -145 TGTCACGC 5.3 5.1e-04 -7.581 3.292 AT1G68875 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -367 -360 GTTTCCGC 5.4 4.2e-04 -7.775 3.377 AT1G68875 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -358 -351 TGTCCCGC 8.1 2.3e-05 -10.680 4.638 PAS2 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -138 -131 TTACCCTC 5.1 7.4e-04 -7.209 3.131 AT1G08057 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -399 -392 TTTCCAGC 7.1 1.4e-04 -8.874 3.854 AT1G08057 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -75 -68 CTTCCCAC 5.1 6.7e-04 -7.308 3.174 AT2G27790 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -413 -406 TCTCCCAC 4.9 8.8e-04 -7.036 3.056 AT2G27790 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -299 -292 TCTCTCGC 5.4 4.2e-04 -7.775 3.377 AT1G04177 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -330 -323 GTACCCGC 6.6 2.6e-04 -8.255 3.585 ABH1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -372 -365 TATCCAGC 5.3 5.1e-04 -7.581 3.292 ABH1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -331 -324 TTTCCCGA 7.1 1.4e-04 -8.874 3.854 ABH1 site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ R -305 -298 TTTCCTGC 7.1 1.4e-04 -8.874 3.854 MENG site 5014_E2Fa_Athamap_20091028__E2Fe_Athamap_20091028_ D -324 -317 TTACCCTC 5.1 7.4e-04 -7.209 3.131 MYB1 site 5015_E2Fb_Athamap_20091028_ D -182 -175 TTTCCCGC 10.7 4.7e-06 -12.268 5.328 MYB1 site 5015_E2Fb_Athamap_20091028_ D -118 -111 TATCCCCC 4.9 7.5e-04 -7.195 3.125 CALS5 site 5015_E2Fb_Athamap_20091028_ D -490 -483 TGTCACGC 5.3 5.1e-04 -7.581 3.292 CALS5 site 5015_E2Fb_Athamap_20091028_ D -27 -20 TTTCCCTC 7.1 1.7e-04 -8.680 3.770 AT1G21770 site 5015_E2Fb_Athamap_20091028_ D -197 -190 TGTCCCCC 4.5 9.4e-04 -6.970 3.027 AT1G21770 site 5015_E2Fb_Athamap_20091028_ D -139 -132 CTTCACGC 5.5 3.6e-04 -7.929 3.444 AT1G21770 site 5015_E2Fb_Athamap_20091028_ D -102 -95 TCTGCCGC 5.3 5.1e-04 -7.581 3.292 AT4G22390 site 5015_E2Fb_Athamap_20091028_ R -395 -388 CTTCCCTC 5.0 6.5e-04 -7.339 3.187 AT4G22390 site 5015_E2Fb_Athamap_20091028_ D -214 -207 TCTCCCGC 8.4 2.1e-05 -10.771 4.678 AT5G50180 site 5015_E2Fb_Athamap_20091028_ D -378 -371 TGTCCCAC 4.7 7.9e-04 -7.143 3.102 AT5G39530 site 5015_E2Fb_Athamap_20091028_ R -369 -362 CTTCCCAC 5.0 6.9e-04 -7.279 3.161 AT3G43150 site 5015_E2Fb_Athamap_20091028_ D -152 -145 TGTCACGC 5.3 5.1e-04 -7.581 3.292 AT1G68875 site 5015_E2Fb_Athamap_20091028_ D -367 -360 GTTTCCGC 5.3 4.4e-04 -7.729 3.357 AT1G68875 site 5015_E2Fb_Athamap_20091028_ R -358 -351 TGTCCCGC 8.3 2.3e-05 -10.680 4.638 PAS2 site 5015_E2Fb_Athamap_20091028_ D -138 -131 TTACCCTC 5.0 6.5e-04 -7.339 3.187 AT1G08057 site 5015_E2Fb_Athamap_20091028_ R -399 -392 TTTCCAGC 7.3 1.3e-04 -8.948 3.886 AT1G08057 site 5015_E2Fb_Athamap_20091028_ R -75 -68 CTTCCCAC 5.0 6.9e-04 -7.279 3.161 AT2G27790 site 5015_E2Fb_Athamap_20091028_ R -413 -406 TCTCCCAC 4.8 7.5e-04 -7.195 3.125 AT2G27790 site 5015_E2Fb_Athamap_20091028_ R -299 -292 TCTCTCGC 5.4 4.4e-04 -7.729 3.357 AT1G04177 site 5015_E2Fb_Athamap_20091028_ R -330 -323 GTACCCGC 6.4 2.6e-04 -8.255 3.585 ABH1 site 5015_E2Fb_Athamap_20091028_ D -372 -365 TATCCAGC 5.3 4.4e-04 -7.729 3.357 ABH1 site 5015_E2Fb_Athamap_20091028_ D -331 -324 TTTCCCGA 7.3 1.3e-04 -8.948 3.886 ABH1 site 5015_E2Fb_Athamap_20091028_ R -305 -298 TTTCCTGC 7.3 1.3e-04 -8.948 3.886 MENG site 5015_E2Fb_Athamap_20091028_ D -324 -317 TTACCCTC 5.0 6.5e-04 -7.339 3.187 PUB24 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -116 -106 GAGCCGCCATT 4.6 8.3e-04 -7.094 3.081 MYB1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -181 -171 TTCCCGCCATA 12.1 2.0e-07 -15.425 6.699 MYB1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -11 -1 ATCCCCCGAAA 6.3 2.1e-04 -8.468 3.678 CALS5 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -26 -16 TTCCCTCTTAA 4.7 7.7e-04 -7.169 3.114 RCCR site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -66 -56 ATCCCGGTAAA 6.1 2.7e-04 -8.217 3.569 AT1G21770 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -138 -128 TTCACGCCAAA 8.8 1.7e-05 -10.982 4.770 AT4G22390 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -399 -389 TTCCCTCGAAT 7.4 8.1e-05 -9.421 4.092 AT4G22390 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -213 -203 CTCCCGCCATT 9.1 1.2e-05 -11.331 4.921 AT5G39530 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -403 -393 TTTCCTCCCTA 5.1 5.4e-04 -7.524 3.268 AT3G43150 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -250 -240 AGCCCGCGAAA 7.9 4.8e-05 -9.944 4.319 AT3G43150 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -249 -239 TTCGCGGGCTC 4.7 8.3e-04 -7.094 3.081 PAS2 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -137 -127 TACCCTCCCAA 7.7 6.1e-05 -9.705 4.215 AT1G08057 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -403 -393 TTCCAGCCCAA 8.7 1.9e-05 -10.871 4.721 AT1G08057 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -148 -138 GTCCCTCCATT 5.3 4.6e-04 -7.684 3.337 AT1G08057 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -79 -69 TTCCCACGCTT 7.4 8.1e-05 -9.421 4.092 AT2G27790 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -301 -291 TTCTCTCGCAA 5.0 6.0e-04 -7.419 3.222 AT1G04177 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -334 -324 TACCCGCCTTA 9.0 1.3e-05 -11.251 4.886 AT1G04177 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -321 -311 TTCCTTCCCAT 4.9 7.2e-04 -7.236 3.143 AT1G04177 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -125 -115 TACGAGCCTTA 4.5 9.1e-04 -7.002 3.041 AT2G30560 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -484 -474 TTGACGCCAAA 5.3 4.6e-04 -7.684 3.337 AAE6 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -192 -182 ATTACGCCAAT 4.4 9.8e-04 -6.928 3.009 AAE6 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -34 -24 TACCTACCCTA 4.8 7.7e-04 -7.169 3.114 ABH1 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ R -309 -299 TTCCTGCAAAT 5.2 5.4e-04 -7.524 3.268 MSR4 site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -417 -407 TATCCGCCATT 7.3 9.0e-05 -9.316 4.046 MENG site 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ D -497 -487 TTGCCGACAAA 5.1 5.4e-04 -7.524 3.268 ; ; 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_ 23 0 ; 2 5015_E2Fb_Athamap_20091028_ 24 0 ; 3 5016_E2Fc_Athamap_20091028__E2Fd_Athamap_20091028_ 25 0 ; TOTAL 72 0 ; Host name rsat ; Job started 2026-08-17.164441 ; Job done 2026-08-17.164442 ; Seconds 0.47 ; user 0.47 ; system 0.04 ; cuser 0.8 ; csystem 0.1